Sandbox Reserved 1687 - Revision history

Cesar Mares at 02:58, 27 October 2021

Cesar Mares — Wed, 27 Oct 2021 02:58:40 GMT

←Older revision		Revision as of 02:58, 27 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription. <scene name='89/891377/Motif_f/1'>Motif F</scene> is composed of several basic residues and is likely involved in RNA binding. There are a number of conserved residues in EBOV RdRp that are involved in template-primer binding (residues 545, 547, 553, 627, 705-706, 708-709, 780, 783, 795-796, 801, 809, 813.<ref>PMID:26397100</ref>	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription. <scene name='89/891377/Motif_f/1'>Motif F</scene> is composed of several basic residues and is likely involved in RNA binding. There are a number of <scene name='89/891377/Template_primer_interactions/1'>conserved residues</scene> in EBOV RdRp that are involved in template-primer binding (residues 545, 547, 553, 627, 705-706, 708-709, 780, 783, 795-796, 801, 809, 813.<ref>PMID:26397100</ref>

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 02:52, 27 October 2021

Cesar Mares — Wed, 27 Oct 2021 02:52:17 GMT

←Older revision		Revision as of 02:52, 27 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription. <scene name='89/891377/Motif_f/1'>Motif F</scene> is composed of several basic residues and is likely involved in RNA binding.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription. <scene name='89/891377/Motif_f/1'>Motif F</scene> is composed of several basic residues and is likely involved in RNA binding. There are a number of conserved residues in EBOV RdRp that are involved in template-primer binding (residues 545, 547, 553, 627, 705-706, 708-709, 780, 783, 795-796, 801, 809, 813.<ref>PMID:26397100</ref>

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 02:38, 27 October 2021

Cesar Mares — Wed, 27 Oct 2021 02:38:06 GMT

←Older revision		Revision as of 02:38, 27 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription. <scene name='89/891377/Motif_f/1'>Motif F</scene> is composed of several basic residues and is likely involved in RNA binding.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 02:34, 27 October 2021

Cesar Mares — Wed, 27 Oct 2021 02:34:26 GMT

←Older revision		Revision as of 02:34, 27 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved residue 624 that is one of two catalytic aspartic acid residues (the other being residue 734 in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved <scene name='89/891377/Cat_residues_624_734/1'>residue 624</scene> that is one of two catalytic aspartic acid residues (the other being <scene name='89/891377/Cat_residues_624_734/1'>residue 734</scene> in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. <scene name='89/891377/Motif_d/1'>Motif D</scene> is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> <scene name='89/891377/Motif_e/1'>Motif E</scene> has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 02:24, 27 October 2021

Cesar Mares — Wed, 27 Oct 2021 02:24:28 GMT

←Older revision		Revision as of 02:24, 27 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved residue 624 that is one of two catalytic aspartic acid residues (the other being residue 734 in motif C).<ref>PMID:26397100</ref> Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved residue 624 that is one of two catalytic aspartic acid residues (the other being residue 734 in motif C).<ref>PMID:26397100</ref> <scene name='89/891377/Motif_b/1'>Motif B</scene> is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. <scene name='89/891377/Motif_c/1'>Motif C</scene> possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 02:11, 27 October 2021

Cesar Mares — Wed, 27 Oct 2021 02:11:50 GMT

←Older revision		Revision as of 02:11, 27 October 2021
Line 12:		Line 12:

	==RNA Classification==		==RNA Classification==
-	Ebola is part of the Filoviridae family of single-stranded negative-sense RNA viruses of approximately 19 kb.<ref>PMID:31567063</ref> The 19 kb RNA encodes for “glycoproteins (i.e., GP, sGP, ssGP), nucleoproteins, virion proteins (i.e., VP 24, 30, 40) and the RNA-dependent RNA polymerase”.<ref>PMID:31806422</ref> In EBOV, the RNA dependent RNA polymerase in conjunction with NP, VP30, and VP35 form the RNP complex in viral genome transcription and replication.<ref>PMID:31806422</ref> ~~RDRP~~ binds to the 3’ leader promoter and changes EBOV’s negative-sense RNA into positive-sense messenger RNA to produce Ebola proteins that produce new viral particles (virions).<ref>PMID:31806422</ref>	+	Ebola is part of the Filoviridae family of single-stranded negative-sense RNA viruses of approximately 19 kb.<ref>PMID:31567063</ref> The 19 kb RNA encodes for “glycoproteins (i.e., GP, sGP, ssGP), nucleoproteins, virion proteins (i.e., VP 24, 30, 40) and the RNA-dependent RNA polymerase”.<ref>PMID:31806422</ref> In EBOV, the RNA-dependent RNA polymerase in conjunction with NP, VP30, and VP35 form the RNP complex in viral genome transcription and replication.<ref>PMID:31806422</ref> RdRp binds to the 3’ leader promoter and changes EBOV’s negative-sense RNA into positive-sense messenger RNA to produce Ebola proteins that produce new viral particles (virions).<ref>PMID:31806422</ref>

	==Function of RNA-Dependent RNA Polymerase==		==Function of RNA-Dependent RNA Polymerase==
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved ~~and~~ catalytic aspartic acid ~~residue found among~~ other ~~RdRp~~. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an ~~Aspartate~~ residue that matches the conserved and catalytic Asp593. The aspartate ~~and asparagine~~ in this model interact with ~~the~~ metal ions and ~~complete~~ the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved residue 624 that is one of two catalytic aspartic acid residues (the other being residue 734 in motif C).<ref>PMID:26397100</ref> Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues.<ref>PMID:26397100</ref> Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 23:20, 26 October 2021

Cesar Mares — Tue, 26 Oct 2021 23:20:45 GMT

←Older revision		Revision as of 23:20, 26 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid residue ~~483~~. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted <scene name='89/891377/Motif_a/1'>motif A</scene> is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid residue found among other RdRp. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 22:55, 26 October 2021

Cesar Mares — Tue, 26 Oct 2021 22:55:02 GMT

←Older revision		Revision as of 22:55, 26 October 2021
Line 19:		Line 19:
	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-E were identified in the palm subdomain of the EBOV RdRp, but motifs ~~F and~~ G, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid 483. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid residue 483. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 20:50, 26 October 2021

Cesar Mares — Tue, 26 Oct 2021 20:50:36 GMT

←Older revision		Revision as of 20:50, 26 October 2021
Line 15:		Line 15:

	==Function of RNA-Dependent RNA Polymerase==		==Function of RNA-Dependent RNA Polymerase==
-	RNA-dependent RNA polymerases (RdRp) are critical to the replication and transcription of RNA viruses.<ref>DOI:10.1038/s41598-018-22328-3</ref> Due to this protein's importance in the viral life cycle, they are feasible targets for vaccine development.<ref>DOI:10.1038/s41598-018-22328-3</ref> Inhibition of RdRp results in the inhibition of transcription of the viral genome, ultimately resulting in no new production of virions for the virus. Without the production of virions, the virus is no longer able to spread.	+	RNA-dependent RNA polymerases (RdRp) are critical to the replication and transcription of RNA viruses.<ref>DOI:10.1038/s41598-018-22328-3</ref> Due to this protein's importance in the viral life cycle, they are feasible targets for vaccine development.<ref>DOI:10.1038/s41598-018-22328-3</ref> There are several antiviral drugs that have been approved that target the EBOV RdRp, including Brincidofovir (CMX-001), Lamivudine and Favipiravir (T-705).<ref>PMID:26397100</ref> Inhibition of RdRp results in the inhibition of transcription of the viral genome, ultimately resulting in no new production of virions for the virus. Without the production of virions, the virus is no longer able to spread.

	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-E were identified in the palm subdomain of the EBOV RdRp, but motifs F and G, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid 483. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-E were identified in the palm subdomain of the EBOV RdRp, but motifs F and G, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid 483. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Cesar Mares at 20:21, 26 October 2021

Cesar Mares — Tue, 26 Oct 2021 20:21:46 GMT

←Older revision		Revision as of 20:21, 26 October 2021
Line 7:		Line 7:
	EVD pathogenesis in humans consists of three phases with symptoms normally occurring after an incubation period of 2-21 days.<ref>PMID:31567063</ref> In the first phase, symptoms during the first few days include nonspecific fever, headache, and myalgia.<ref>PMID:31567063</ref> This is followed by a “gastrointestinal phase” characterized by symptoms including diarrhea, vomiting, abdominal discomfort, and dehydration.<ref>PMID:31567063</ref> The final and advanced phase of the illness consist of kidney and liver function failure, often resulting in “metabolic compromise, convulsion, shock, and death due to mucosal bleeding, bloody diarrhea, and multi-organ failure within 16 days after the first symptoms appear”.<ref>PMID:31567063</ref>		EVD pathogenesis in humans consists of three phases with symptoms normally occurring after an incubation period of 2-21 days.<ref>PMID:31567063</ref> In the first phase, symptoms during the first few days include nonspecific fever, headache, and myalgia.<ref>PMID:31567063</ref> This is followed by a “gastrointestinal phase” characterized by symptoms including diarrhea, vomiting, abdominal discomfort, and dehydration.<ref>PMID:31567063</ref> The final and advanced phase of the illness consist of kidney and liver function failure, often resulting in “metabolic compromise, convulsion, shock, and death due to mucosal bleeding, bloody diarrhea, and multi-organ failure within 16 days after the first symptoms appear”.<ref>PMID:31567063</ref>

-	Since EBOV's discovery, there have been 20 known outbreaks restricted primarily to African countries with minor spread to neighboring countries.<ref>PMID:30777297</ref> The most recent outbreak of Ebola occurred during a three-month span in the Democratic Republic of the Congo this year, the country’s 4th in the past three years.[https://news.un.org/en/story/2021/05/1091162] Since its start in February, there was a total of eleven confirmed cases with six recoveries and six deaths and one probable case emanating from four health zones in North Kivu.[https://news.un.org/en/story/2021/05/1091162] There is also an ongoing outbreak in Guinea, West Africa which started in the same month as the outbreak in the DRC.[https://news.un.org/en/story/2021/05/1091162]	+	Since EBOV's discovery, there have been 20 known outbreaks restricted primarily to African countries with minor spread to neighboring countries.<ref>PMID:30777297</ref> The most recent outbreak of Ebola occurred during a three-month span in the Democratic Republic of the Congo this year (2021), the country’s 4th in the past three years.[https://news.un.org/en/story/2021/05/1091162] Since its start in February, there was a total of eleven confirmed cases with six recoveries and six deaths and one probable case emanating from four health zones in North Kivu.[https://news.un.org/en/story/2021/05/1091162] There is also an ongoing outbreak in Guinea, West Africa which started in the same month as the outbreak in the DRC.[https://news.un.org/en/story/2021/05/1091162]

	There is currently no vaccine for EVD, but there are currently eight vaccine candidates in human clinical trials that all target the Ebola virus glycoprotein (GP), one of the nine known proteins to be expressed by the virus’s genome.<ref>PMID:31567063</ref> However, these vaccines are different from each other in the immune responses they elicit, the antigen delivery system, and their respective side-effect profiles.<ref>PMID:31567063</ref>		There is currently no vaccine for EVD, but there are currently eight vaccine candidates in human clinical trials that all target the Ebola virus glycoprotein (GP), one of the nine known proteins to be expressed by the virus’s genome.<ref>PMID:31567063</ref> However, these vaccines are different from each other in the immune responses they elicit, the antigen delivery system, and their respective side-effect profiles.<ref>PMID:31567063</ref>
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	==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==		==Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[https://swissmodel.expasy.org/interactive/7EhwKr/]==

-	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/1'>right-hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/4'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/5'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/1'>thumb</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-E were identified in the palm subdomain of the EBOV RdRp, but motifs F and G, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid 483. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.	+	EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic <scene name='89/891377/Rh_shape/4'>right hand shape</scene> of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. <ref>PMID:26397100</ref> The 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [https://swissmodel.expasy.org/interactive/7EhwKr/] The <scene name='89/891377/Fingertips_subdomain_2/9'>fingertips subdomain</scene> is composed of residues 417-439 and 489-563, the <scene name='89/891377/Palm_subdomain_1/7'>palm subdomain</scene> is composed of residues 440-488 and 563-666, and the <scene name='89/891377/Thumb_subdomain/4'>thumb subdomain</scene> is made up of residues 667-704.<ref>PMID:26397100</ref> The highly conserved motifs A-E were identified in the palm subdomain of the EBOV RdRp, but motifs F and G, which are not part of the active site, were not identified.<ref>PMID:26397100</ref> The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved and catalytic aspartic acid 483. Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an Aspartate residue that matches the conserved and catalytic Asp593. The aspartate and asparagine in this model interact with the metal ions and complete the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>