4e7k - Revision history

OCA at 14:54, 14 March 2024

2024-03-14T14:54:44Z

← Older revision		Revision as of 14:54, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E7K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.02Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [https://pdbe.org/4e7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [https://www.ebi.ac.uk/pdbsum/4e7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e7k 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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [https://pdbe.org/4e7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [https://www.ebi.ac.uk/pdbsum/4e7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e7k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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-Lys1,2 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 and near the center 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 primer. 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 at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. 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. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).		[https://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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-Lys1,2 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 and near the center 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 primer. 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 at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. 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. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Retroviral integrase (IN) is responsible for two consecutive reactions, which lead to insertion of a viral DNA copy into a host cell chromosome. Initially, the enzyme removes di- or trinucleotides from viral DNA ends to expose 3'-hydroxyls attached to the invariant CA dinucleotides (3'-processing reaction). Second, it inserts the processed 3'-viral DNA ends into host chromosomal DNA (strand transfer). Herein, we report a crystal structure of prototype foamy virus IN bound to viral DNA prior to 3'-processing. Furthermore, taking advantage of its dependence on divalent metal ion cofactors, we were able to freeze trap the viral enzyme in its ground states containing all the components necessary for 3'-processing or strand transfer. Our results shed light on the mechanics of retroviral DNA integration and explain why HIV IN strand transfer inhibitors are ineffective against the 3'-processing step of integration. The ground state structures moreover highlight a striking substrate mimicry utilized by the inhibitors in their binding to the IN active site and suggest ways to improve upon this clinically relevant class of small molecules.

	3'-Processing and strand transfer catalysed by retroviral integrase in crystallo.,Hare S, Maertens GN, Cherepanov P EMBO J. 2012 May 11. doi: 10.1038/emboj.2012.118. PMID:22580823<ref>PMID:22580823</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e7k" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]		*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:55, 28 September 2022

2022-09-28T06:55:31Z

← Older revision		Revision as of 06:55, 28 September 2022
Line 1:		Line 1:

	==PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution==		==PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution==
	<StructureSection load='4e7k' size='340' side='right' caption='[[4e7k]], [[Resolution\|resolution]] 3.02Å' scene=''>		<StructureSection load='4e7k' size='340' side='right'caption='[[4e7k]], [[Resolution\|resolution]] 3.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Foamv Foamv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E7K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlr\|3dlr]], [[3oy9\|3oy9]], [[3oya\|3oya]], [[3os2\|3os2]]</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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [https://pdbe.org/4e7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [https://www.ebi.ac.uk/pdbsum/4e7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e7k ProSAT]</span></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 FOAMV])~~</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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [~~http~~://pdbe.org/4e7k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e7k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e7k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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-Lys1,2 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 and near the center 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 primer. 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 at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. 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. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).		[[https://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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-Lys1,2 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 and near the center 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 primer. 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 at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. 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. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]
			*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Foamv~~]]		[[Category: Human spumaretrovirus]]
	[[Category: ~~Cherepanov, P~~]]		[[Category: Large Structures]]
	[[Category: ~~Maertens, G N~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Dna-binding~~]]		[[Category: Cherepanov P]]
	[[Category: ~~Endonuclease]]~~		[[Category: Maertens GN]]
	~~[[Category: Hhcc motif]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Multifunctional enzyme]]~~
	~~[[Category: Nuclease]]~~
	~~[[Category: Nucleotidyltransferase]]~~
	~~[[Category: Nucleus]]~~
	~~[[Category: Protein-dna complex]]~~
	~~[[Category: Recombination]]~~
	~~[[Category: Recombination-dna complex]]~~
	~~[[Category: Tetramer]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Viral protein]]~~
	~~[[Category: Viral protein-dna complex]]~~
	~~[[Category: Virion]]~~
	~~[[Category: Zinc-binding~~]]

OCA at 19:10, 5 August 2016

2016-08-05T19:10:42Z

← Older revision		Revision as of 19:10, 5 August 2016
Line 1:		Line 1:

	==PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution==		==PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution==
	<StructureSection load='4e7k' size='340' side='right' caption='[[4e7k]], [[Resolution\|resolution]] 3.02Å' scene=''>		<StructureSection load='4e7k' size='340' side='right' caption='[[4e7k]], [[Resolution\|resolution]] 3.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_spumaretrovirus Human spumaretrovirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Foamv Foamv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E7K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlr\|3dlr]], [[3oy9\|3oy9]], [[3oya\|3oya]], [[3os2\|3os2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlr\|3dlr]], [[3oy9\|3oy9]], [[3oya\|3oya]], [[3os2\|3os2]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 ~~Human spumaretrovirus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 FOAMV])</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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [http://www.ebi.ac.uk/pdbsum/4e7k 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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [http://pdbe.org/4e7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [http://www.ebi.ac.uk/pdbsum/4e7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e7k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4e7k" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Ribonuclease\|Ribonuclease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human spumaretrovirus~~]]		[[Category: Foamv]]
	[[Category: Cherepanov, P]]		[[Category: Cherepanov, P]]
	[[Category: Maertens, G N]]		[[Category: Maertens, G N]]

OCA at 05:06, 25 December 2014

2014-12-25T05:06:05Z

← Older revision		Revision as of 05:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E7K FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlr\|3dlr]], [[3oy9\|3oy9]], [[3oya\|3oya]], [[3os2\|3os2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlr\|3dlr]], [[3oy9\|3oy9]], [[3oya\|3oya]], [[3os2\|3os2]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 Human spumaretrovirus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 Human spumaretrovirus])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [http://www.ebi.ac.uk/pdbsum/4e7k 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=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [http://www.ebi.ac.uk/pdbsum/4e7k PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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-Lys1,2 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 and near the center 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 primer. 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 at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. 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. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Human spumaretrovirus]]		[[Category: Human spumaretrovirus]]
	[[Category: Cherepanov, P.]]		[[Category: Cherepanov, P]]
	[[Category: Maertens, G N.]]		[[Category: Maertens, G N]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 08:18, 5 June 2014

2014-06-05T08:18:32Z

← Older revision		Revision as of 08:18, 5 June 2014
Line 1:		Line 1:
	[[~~Image~~:~~4e7k~~.~~png~~\|~~left~~\|~~200px~~]]		==PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution==
			<StructureSection load='4e7k' size='340' side='right' caption='[[4e7k]], [[Resolution\|resolution]] 3.02Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e7k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E7K FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlr\|3dlr]], [[3oy9\|3oy9]], [[3oya\|3oya]], [[3os2\|3os2]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 Human spumaretrovirus])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e7k RCSB], [http://www.ebi.ac.uk/pdbsum/4e7k PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Retroviral integrase (IN) is responsible for two consecutive reactions, which lead to insertion of a viral DNA copy into a host cell chromosome. Initially, the enzyme removes di- or trinucleotides from viral DNA ends to expose 3'-hydroxyls attached to the invariant CA dinucleotides (3'-processing reaction). Second, it inserts the processed 3'-viral DNA ends into host chromosomal DNA (strand transfer). Herein, we report a crystal structure of prototype foamy virus IN bound to viral DNA prior to 3'-processing. Furthermore, taking advantage of its dependence on divalent metal ion cofactors, we were able to freeze trap the viral enzyme in its ground states containing all the components necessary for 3'-processing or strand transfer. Our results shed light on the mechanics of retroviral DNA integration and explain why HIV IN strand transfer inhibitors are ineffective against the 3'-processing step of integration. The ground state structures moreover highlight a striking substrate mimicry utilized by the inhibitors in their binding to the IN active site and suggest ways to improve upon this clinically relevant class of small molecules.

	~~{{STRUCTURE_4e7k\| PDB=4e7k \| SCENE= }}~~		3'-Processing and strand transfer catalysed by retroviral integrase in crystallo.,Hare S, Maertens GN, Cherepanov P EMBO J. 2012 May 11. doi: 10.1038/emboj.2012.118. PMID:22580823<ref>PMID:22580823</ref>

	~~===PFV integrase Target Capture Complex (TCC-Mn)~~, ~~freeze-trapped prior to strand transfer, at 3.0 A resolution===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22580823}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[4e7k]] is~~ a ~~5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4E7K OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:022580823<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Human spumaretrovirus]]		[[Category: Human spumaretrovirus]]
	[[Category: Cherepanov, P.]]		[[Category: Cherepanov, P.]]

OCA at 06:16, 25 July 2012

2012-07-25T06:16:31Z

← Older revision		Revision as of 06:16, 25 July 2012
Line 1:		Line 1:
	[[Image:4e7k.~~jpg~~\|left\|200px]]		[[Image:4e7k.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_4e7k", 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_4e7k\| PDB=4e7k \| SCENE= }}		{{STRUCTURE_4e7k\| PDB=4e7k \| SCENE= }}

	===PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution===		===PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22580823}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 22580823 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_22580823}}		{{ABSTRACT_PUBMED_22580823}}

OCA at 06:07, 23 May 2012

2012-05-23T06:07:37Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4e7k.jpg|left|200px]]
-The entry 4e7k is ON HOLD  until Paper Publication
+<!--
-Authors: Maertens, G.N., Cherepanov, P.
+===PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution===
-Description: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution

OCA at 06:39, 11 April 2012

2012-04-11T06:39:20Z

← Older revision		Revision as of 06:39, 11 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e7k is ON HOLD		The entry 4e7k is ON HOLD until Paper Publication

	Authors: Maertens, G.N., Cherepanov, P.		Authors: Maertens, G.N., Cherepanov, P.

	Description: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution		Description: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution

OCA: Protected "4e7k" [edit=sysop:move=sysop]

2012-03-28T07:23:28Z

Protected "4e7k" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:23, 28 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e7k is ON HOLD Authors: Maertens, G.N., Cherepanov, P. Description: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand ...

2012-03-28T07:23:27Z

New page: '''Unreleased structure''' The entry 4e7k is ON HOLD Authors: Maertens, G.N., Cherepanov, P. Description: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand ...

New page

'''Unreleased structure'''

The entry 4e7k is ON HOLD

Authors: Maertens, G.N., Cherepanov, P.

Description: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution