6b1q - Revision history

OCA at 14:30, 4 October 2023

OCA — Wed, 04 Oct 2023 14:30:32 GMT

←Older revision		Revision as of 14:30, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6b1q' size='340' side='right'caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6b1q' size='340' side='right'caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mlvmo Mlvmo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=1AP:2,6~~-~~DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>~~, ~~<scene name='pdbligand=CJ1:'>CJ1</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase]~~, ~~with EC number [http~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~2~~.7.7.49~~ 2~~.7.7.49~~] </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CJ1:7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diol'>CJ1</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6b1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b1q OCA], [~~http~~://pdbe.org/6b1q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b1q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b1q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b1q 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=6b1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b1q OCA], [https://pdbe.org/6b1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b1q RCSB], [https://www.ebi.ac.uk/pdbsum/6b1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b1q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/POL_MLVMS POL_MLVMS]] Gag-Pol polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release. Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome (By similarity).	+	[https://www.uniprot.org/uniprot/POL_MLVMS POL_MLVMS] Gag-Pol polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release. Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mlvmo]]~~	+	[[Category: Moloney murine leukemia virus]]
-	~~[[Category: RNA-directed DNA polymerase~~]]	+	[[Category: Georgiadis MM]]
-	[[Category: Georgiadis~~, M M~~]]	+	[[Category: Singh I]]
-	[[Category: Singh, I]]	+
-	~~[[Category: Aegis]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Host-guest system]]~~	+
-	~~[[Category: Protein-dna]]~~	+
-	~~[[Category: Unnatural base pair~~]]	+

OCA at 21:35, 28 October 2020

OCA — Wed, 28 Oct 2020 21:35:23 GMT

←Older revision		Revision as of 21:35, 28 October 2020
Line 1:		Line 1:

	==Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix==		==Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix==
-	<StructureSection load='6b1q' size='340' side='right' caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6b1q' size='340' side='right'caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mlvmo Mlvmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mlvmo Mlvmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CJ1:'>CJ1</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CJ1:'>CJ1</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] </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=6b1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b1q OCA], [http://pdbe.org/6b1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b1q RCSB], [http://www.ebi.ac.uk/pdbsum/6b1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b1q ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6b1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b1q OCA], [http://pdbe.org/6b1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b1q RCSB], [http://www.ebi.ac.uk/pdbsum/6b1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b1q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6b1q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6b1q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Reverse transcriptase 3D structures\|Reverse transcriptase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mlvmo]]		[[Category: Mlvmo]]
	[[Category: RNA-directed DNA polymerase]]		[[Category: RNA-directed DNA polymerase]]

OCA at 08:37, 26 September 2018

OCA — Wed, 26 Sep 2018 08:37:40 GMT

←Older revision		Revision as of 08:37, 26 September 2018
Line 3:		Line 3:
	<StructureSection load='6b1q' size='340' side='right' caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6b1q' size='340' side='right' caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mlvmo Mlvmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CJ1:'>CJ1</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CJ1:'>CJ1</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] </span></td></tr>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mlvmo]]
	[[Category: RNA-directed DNA polymerase]]		[[Category: RNA-directed DNA polymerase]]
	[[Category: Georgiadis, M M]]		[[Category: Georgiadis, M M]]

OCA at 19:44, 19 September 2018

OCA — Wed, 19 Sep 2018 19:44:28 GMT

←Older revision		Revision as of 19:44, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~6b1q~~ is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix==
		+	<StructureSection load='6b1q' size='340' side='right' caption='[[6b1q]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6b1q]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B1Q FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CJ1:'>CJ1</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] </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=6b1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b1q OCA], [http://pdbe.org/6b1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b1q RCSB], [http://www.ebi.ac.uk/pdbsum/6b1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b1q ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POL_MLVMS POL_MLVMS]] Gag-Pol polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release. Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our understanding of alternative ways that genetic information might be stored and transmitted.

-	~~Authors~~: ~~Singh~~, I., Georgiadis, M.M.	+	"Skinny" and "Fat" DNA: Two New Double Helices.,Hoshika S, Singh I, Switzer C, Molt RW Jr, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA J Am Chem Soc. 2018 Sep 10. doi: 10.1021/jacs.8b05042. PMID:30148365<ref>PMID:30148365</ref>

-	~~Description: Hydrogen Bonding Complementary~~, ~~not size complementarity is key in the formation~~ of the ~~double helix~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6b1q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RNA-directed DNA polymerase]]
		+	[[Category: Georgiadis, M M]]
	[[Category: Singh, I]]		[[Category: Singh, I]]
-	[[Category: ~~Georgiadis, M.M~~]]	+	[[Category: Aegis]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Host-guest system]]
		+	[[Category: Protein-dna]]
		+	[[Category: Unnatural base pair]]

OCA at 04:50, 1 November 2017

OCA — Wed, 01 Nov 2017 04:50:42 GMT

←Older revision		Revision as of 04:50, 1 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6b1q is ON HOLD	+	The entry 6b1q is ON HOLD until Paper Publication

	Authors: Singh, I., Georgiadis, M.M.		Authors: Singh, I., Georgiadis, M.M.

OCA: Protected "6b1q" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 17:04:20 GMT

Protected "6b1q" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:04, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6b1q is ON HOLD Authors: Singh, I., Georgiadis, M.M. Description: Hydrogen Bonding Complementary, not size complementarity is key in the formation ...

OCA — Wed, 27 Sep 2017 17:04:19 GMT

New page: '''Unreleased structure''' The entry 6b1q is ON HOLD Authors: Singh, I., Georgiadis, M.M. Description: Hydrogen Bonding Complementary, not size complementarity is key in the formation ...

New page

'''Unreleased structure'''

The entry 6b1q is ON HOLD

Authors: Singh, I., Georgiadis, M.M.

Description: Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix
[[Category: Unreleased Structures]]
[[Category: Singh, I]]
[[Category: Georgiadis, M.M]]