3gpo - Revision history

OCA at 07:09, 6 September 2023

2023-09-06T07:09:40Z

←Older revision		Revision as of 07:09, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3gpo' size='340' side='right'caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3gpo' size='340' side='right'caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Chiks Chiks~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chikungunya_virus_strain_S27-African_prototype Chikungunya virus strain S27-African prototype]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=APR:ADENOSINE~~-~~5-DIPHOSPHORIBOSE'>APR</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3gpg\|3gpg]], [[3gpq\|3gpq]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371094 CHIKS])~~</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [https://pdbe.org/3gpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [https://www.ebi.ac.uk/pdbsum/3gpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpo ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [https://pdbe.org/3gpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [https://www.ebi.ac.uk/pdbsum/3gpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLN_CHIKS POLN_CHIKS]] P123 is short-lived polyproteins, accumulating during early stage of infection. It localizes the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, it starts viral genome replication into antigenome. After these early events, P123 is cleaved sequentially into nsP1, nsP2 and nsP3. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity). nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins (By similarity). Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis (By similarity). nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins (By similarity).	+	[https://www.uniprot.org/uniprot/POLN_CHIKS POLN_CHIKS] P123 is short-lived polyproteins, accumulating during early stage of infection. It localizes the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, it starts viral genome replication into antigenome. After these early events, P123 is cleaved sequentially into nsP1, nsP2 and nsP3. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity). nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins (By similarity). Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis (By similarity). nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chiks~~]]	+	[[Category: Chikungunya virus strain S27-African prototype]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Canard, B]]	+	[[Category: Canard B]]
-	[[Category: Coutard, B]]	+	[[Category: Coutard B]]
-	[[Category: Jamal, S]]	+	[[Category: Jamal S]]
-	[[Category: Malet, H]]	+	[[Category: Malet H]]
-	~~[[Category: Adp-ribose]]~~	+
-	~~[[Category: Alphavirus]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Chikungunya]]~~	+
-	~~[[Category: Endosome]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lipoprotein]]~~	+
-	~~[[Category: Lysosome]]~~	+
-	~~[[Category: Macro domain]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Mrna capping]]~~	+
-	~~[[Category: Mrna processing]]~~	+
-	~~[[Category: Multifunctional enzyme]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Palmitate]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Rna replication]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rna-directed rna polymerase]]~~	+
-	~~[[Category: Thiol protease]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virus]]~~	+
-	~~[[Category: Vizier. viral enzymes involved in replication]]~~	+
-	~~[[Category: X domain~~]]	+

OCA at 07:51, 16 March 2022

2022-03-16T07:51:50Z

←Older revision		Revision as of 07:51, 16 March 2022
Line 1:		Line 1:

	==Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose==		==Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose==
-	<StructureSection load='3gpo' size='340' side='right' caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3gpo' size='340' side='right'caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Chiks Chiks]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chiks Chiks]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpg\|3gpg]], [[3gpq\|3gpq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gpg\|3gpg]], [[3gpq\|3gpq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371094 CHIKS])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371094 CHIKS])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [~~http~~://pdbe.org/3gpo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gpo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpo ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [https://pdbe.org/3gpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [https://www.ebi.ac.uk/pdbsum/3gpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLN_CHIKS POLN_CHIKS]] P123 is short-lived polyproteins, accumulating during early stage of infection. It localizes the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, it starts viral genome replication into antigenome. After these early events, P123 is cleaved sequentially into nsP1, nsP2 and nsP3. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity). nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins (By similarity). Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis (By similarity). nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins (By similarity).	+	[[https://www.uniprot.org/uniprot/POLN_CHIKS POLN_CHIKS]] P123 is short-lived polyproteins, accumulating during early stage of infection. It localizes the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, it starts viral genome replication into antigenome. After these early events, P123 is cleaved sequentially into nsP1, nsP2 and nsP3. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity). nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins (By similarity). Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis (By similarity). nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Chiks]]		[[Category: Chiks]]
		+	[[Category: Large Structures]]
	[[Category: Canard, B]]		[[Category: Canard, B]]
	[[Category: Coutard, B]]		[[Category: Coutard, B]]

OCA at 05:31, 7 December 2018

2018-12-07T05:31:22Z

←Older revision		Revision as of 05:31, 7 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose==		==Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose==
	<StructureSection load='3gpo' size='340' side='right' caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3gpo' size='340' side='right' caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpg\|3gpg]], [[3gpq\|3gpq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpg\|3gpg]], [[3gpq\|3gpq]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371094 CHIKS])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371094 CHIKS])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://pdbe.org/3gpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://pdbe.org/3gpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpo_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 04:38, 10 February 2016

2016-02-10T04:38:19Z

←Older revision		Revision as of 04:38, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3gpo' size='340' side='right' caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3gpo' size='340' side='right' caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Chikungunya_virus Chikungunya virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chiks Chiks]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpg\|3gpg]], [[3gpq\|3gpq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpg\|3gpg]], [[3gpq\|3gpq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~37124 Chikungunya virus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371094 CHIKS])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://pdbe.org/3gpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gpo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3gpo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chikungunya virus~~]]	+	[[Category: Chiks]]
	[[Category: Canard, B]]		[[Category: Canard, B]]
	[[Category: Coutard, B]]		[[Category: Coutard, B]]

OCA at 11:50, 25 December 2014

2014-12-25T11:50:31Z

←Older revision		Revision as of 11:50, 25 December 2014
Line 9:		Line 9:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLN_CHIKS POLN_CHIKS]] P123 is short-lived polyproteins, accumulating during early stage of infection. It localizes the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, it starts viral genome replication into antigenome. After these early events, P123 is cleaved sequentially into nsP1, nsP2 and nsP3. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity). nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins (By similarity). Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis (By similarity). nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:05, 8 December 2014

2014-12-08T09:05:29Z

←Older revision		Revision as of 09:05, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3gpo.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose==
		+	<StructureSection load='3gpo' size='340' side='right' caption='[[3gpo]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chikungunya_virus Chikungunya virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpg\|3gpg]], [[3gpq\|3gpq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nsP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37124 Chikungunya virus])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpo RCSB], [http://www.ebi.ac.uk/pdbsum/3gpo PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpo_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Macro domains (also called "X domains") constitute a protein module family present in all kingdoms of life, including viruses of the Coronaviridae and Togaviridae families. Crystal structures of the macro domain from the Chikungunya virus (an "Old World" alphavirus) and the Venezuelan equine encephalitis virus (a "New World" alphavirus) were determined at resolutions of 1.65 and 2.30 A, respectively. These domains are active as adenosine di-phosphoribose 1''-phosphate phosphatases. Both the Chikungunya and the Venezuelan equine encephalitis virus macro domains are ADP-ribose binding modules, as revealed by structural and functional analysis. A single aspartic acid conserved through all macro domains is responsible for the specific binding of the adenine base. Sequence-unspecific binding to long, negatively charged polymers such as poly(ADP-ribose), DNA, and RNA is observed and attributed to positively charged patches outside of the active site pocket, as judged by mutagenesis and binding studies. The crystal structure of the Chikungunya virus macro domain with an RNA trimer shows a binding mode utilizing the same adenine-binding pocket as ADP-ribose, but avoiding the ADP-ribose 1''-phosphate phosphatase active site. This leaves the AMP binding site as the sole common feature in all macro domains.

-	~~{{STRUCTURE_3gpo\| PDB=3gpo \| SCENE= }}~~	+	The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket.,Malet H, Coutard B, Jamal S, Dutartre H, Papageorgiou N, Neuvonen M, Ahola T, Forrester N, Gould EA, Lafitte D, Ferron F, Lescar J, Gorbalenya AE, de Lamballerie X, Canard B J Virol. 2009 Jul;83(13):6534-45. Epub 2009 Apr 22. PMID:19386706<ref>PMID:19386706</ref>

-	~~===Crystal structure~~ of ~~macro domain of Chikungunya virus in complex with ADP-ribose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19386706}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3gpo]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Chikungunya_virus Chikungunya virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019386706<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Chikungunya virus]]		[[Category: Chikungunya virus]]
-	[[Category: Canard, B.]]	+	[[Category: Canard, B]]
-	[[Category: Coutard, B.]]	+	[[Category: Coutard, B]]
-	[[Category: Jamal, S.]]	+	[[Category: Jamal, S]]
-	[[Category: Malet, H.]]	+	[[Category: Malet, H]]
	[[Category: Adp-ribose]]		[[Category: Adp-ribose]]
	[[Category: Alphavirus]]		[[Category: Alphavirus]]

OCA: Protected "3gpo" [edit=sysop:move=sysop]

2013-02-27T15:39:21Z

Protected "3gpo" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:39, 27 February 2013

OCA at 15:39, 27 February 2013

2013-02-27T15:39:18Z

←Older revision		Revision as of 15:39, 27 February 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3gpo.png\|left\|200px]]
-	[[Image:3gpo.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gpo", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3gpo\| PDB=3gpo \| SCENE= }}		{{STRUCTURE_3gpo\| PDB=3gpo \| SCENE= }}

	===Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose===		===Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19386706}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19386706 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19386706}}		{{ABSTRACT_PUBMED_19386706}}

	==About this Structure==		==About this Structure==
-	~~3GPO~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Chikungunya_virus Chikungunya virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA].	+	[[3gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chikungunya_virus Chikungunya virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19386706~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019386706</ref><references group="xtra"/>
	[[Category: Chikungunya virus]]		[[Category: Chikungunya virus]]
	[[Category: Canard, B.]]		[[Category: Canard, B.]]
Line 34:		Line 22:
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Chikungunya]]		[[Category: Chikungunya]]
-	[[Category: Cytoplasm]]
	[[Category: Endosome]]		[[Category: Endosome]]
	[[Category: Helicase]]		[[Category: Helicase]]
Line 57:		Line 44:
	[[Category: Thiol protease]]		[[Category: Thiol protease]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Ubl conjugation]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
	[[Category: Virus]]		[[Category: Virus]]
	[[Category: Vizier. viral enzymes involved in replication]]		[[Category: Vizier. viral enzymes involved in replication]]
	[[Category: X domain]]		[[Category: X domain]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:38:09 2009''

OCA at 17:38, 22 July 2009

2009-07-22T17:38:11Z

←Older revision		Revision as of 17:38, 22 July 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3gpo.jpg\|left\|200px]]

-	The ~~entry 3gpo~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3gpo", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3gpo\| PDB=3gpo \| SCENE= }}

-	~~Authors: Malet, H., Jamal, S., Coutard, B., Canard, B.~~	+	===Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose===

-	Description: Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May 13 09~~:33:10 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19386706}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19386706 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19386706}}
		+
		+	==About this Structure==
		+	3GPO is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Chikungunya_virus Chikungunya virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPO OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19386706</ref><references group="xtra"/>
		+	[[Category: Chikungunya virus]]
		+	[[Category: Canard, B.]]
		+	[[Category: Coutard, B.]]
		+	[[Category: Jamal, S.]]
		+	[[Category: Malet, H.]]
		+	[[Category: Adp-ribose]]
		+	[[Category: Alphavirus]]
		+	[[Category: Atp-binding]]
		+	[[Category: Cell membrane]]
		+	[[Category: Chikungunya]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Endosome]]
		+	[[Category: Helicase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lipoprotein]]
		+	[[Category: Lysosome]]
		+	[[Category: Macro domain]]
		+	[[Category: Membrane]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Mrna capping]]
		+	[[Category: Mrna processing]]
		+	[[Category: Multifunctional enzyme]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Nucleus]]
		+	[[Category: Palmitate]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Protease]]
		+	[[Category: Rna replication]]
		+	[[Category: Rna-binding]]
		+	[[Category: Rna-directed rna polymerase]]
		+	[[Category: Thiol protease]]
		+	[[Category: Transferase]]
		+	[[Category: Ubl conjugation]]
		+	[[Category: Viral protein]]
		+	[[Category: Virus]]
		+	[[Category: Vizier. viral enzymes involved in replication]]
		+	[[Category: X domain]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:38:09 2009''

OCA at 06:33, 13 May 2009

2009-05-13T06:33:11Z

←Older revision		Revision as of 06:33, 13 May 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3gpo is ON HOLD	+	The entry 3gpo is ON HOLD until Paper Publication

	Authors: Malet, H., Jamal, S., Coutard, B., Canard, B.		Authors: Malet, H., Jamal, S., Coutard, B., Canard, B.
Line 7:		Line 7:
	Description: Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose		Description: Crystal structure of macro domain of Chikungunya virus in complex with ADP-ribose

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 15~~ 09:55:54 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 13 09:33:10 2009''