1yha - Revision history

OCA at 08:57, 14 February 2024

OCA — Wed, 14 Feb 2024 08:57:23 GMT

←Older revision		Revision as of 08:57, 14 February 2024
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	<StructureSection load='1yha' size='340' side='right'caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1yha' size='340' side='right'caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpf1 Bpf1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
-	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [https://pdbe.org/1yha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [https://www.ebi.ac.uk/pdbsum/1yha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yha ProSAT]</span></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]] 2.5Å</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [https://pdbe.org/1yha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [https://www.ebi.ac.uk/pdbsum/1yha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/G5P_BPF1 G5P_BPF1]] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).	+	[https://www.uniprot.org/uniprot/G5P_BPF1 G5P_BPF1] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1yha 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=1yha ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Gene V protein (GVP) encoded by the filamentous phage Ff (M13, fl, fd) is a homodimeric protein of 87 amino acids that binds to single-stranded DNA (ssDNA) nonspecifically and cooperatively. The structure (monoclinic C2 form) of the wild-type protein has been determined and refined at 1.8-A resolution [Skinner et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 2071-2075]. The monomer structure consists of a somewhat distorted five-stranded beta-barrel core with three prominent loops: a DNA-binding loop, a dyad loop, and a dimer contact loop. The amino acid residue at position 41 plays an important role in the dimer-dimer interactions of the protein-ssDNA complex. Two Y41 mutant structures have been studied by X-ray crystallography. The Y41F GVP structure has been refined to an R-factor of 0.180 at 2.2-A resolution and is very similar to the wild-type (wt) structure (rmsd of all C alpha atoms = 0.30 A). In contrast, Y41H GVP forms a new crystal lattice in the space group P2(1)2(1)2(1) with a = 77.18 A, b = 84.17 A, and c = 28.62 A. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-A resolution. The two monomers of Y41H are crystallographically independent, and their structures remain similar to wt-GVP but with significant differences, particularly in the DNA-binding hairpin region. In both crystals, the loop (residues 36-43) that contains the Y41 residue is involved in the crystal dimer packings but in a different manner. The dimer-dimer contacts found in the wt-GVP crystal may be important for GVP aggregation in the absence of DNA. In the presence of DNA, the dimer-dimer contacts may switch to the type found in the Y41H crystal, allowing the GVP-ssDNA complex to form cooperatively. A model of the complex, consistent with existing biochemical and biophysical data, has been constructed from those crystal packing data.
-
-	Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex.,Guan Y, Zhang H, Konings RN, Hilbers CW, Terwilliger TC, Wang AH Biochemistry. 1994 Jun 28;33(25):7768-78. PMID:8011642<ref>PMID:8011642</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yha" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Single-stranded DNA-binding protein 3D structures\|Single-stranded DNA-binding protein 3D structures]]		*[[Single-stranded DNA-binding protein 3D structures\|Single-stranded DNA-binding protein 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpf1~~]]	+	[[Category: Enterobacteria phage f1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Guan, Y]]	+	[[Category: Guan Y]]
-	[[Category: Hilbers~~, C W~~]]	+	[[Category: Hilbers CW]]
-	[[Category: Konings~~, R N.H~~]]	+	[[Category: Konings RNH]]
-	[[Category: Terwilliger~~, T C~~]]	+	[[Category: Terwilliger TC]]
-	[[Category: Wang~~, A H.~~J]]	+	[[Category: Wang AH-J]]
-	[[Category: Zhang, H]]	+	[[Category: Zhang H]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna-binding protein~~]]	+

OCA at 06:33, 6 October 2021

OCA — Wed, 06 Oct 2021 06:33:26 GMT

←Older revision		Revision as of 06:33, 6 October 2021
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	<StructureSection load='1yha' size='340' side='right'caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1yha' size='340' side='right'caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YHA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
-	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [~~http~~://pdbe.org/1yha PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yha PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yha ProSAT]</span></td></tr>	+	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [https://pdbe.org/1yha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [https://www.ebi.ac.uk/pdbsum/1yha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/G5P_BPF1 G5P_BPF1]] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).	+	[[https://www.uniprot.org/uniprot/G5P_BPF1 G5P_BPF1]] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]	+	*[[Single-stranded DNA-binding protein 3D structures\|Single-stranded DNA-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:24, 4 December 2019

OCA — Wed, 04 Dec 2019 11:24:09 GMT

←Older revision		Revision as of 11:24, 4 December 2019
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	==CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX==		==CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX==
-	<StructureSection load='1yha' size='340' side='right' caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1yha' size='340' side='right'caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yh/1yha_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yh/1yha_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>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1yha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1yha" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bpf1]]		[[Category: Bpf1]]
		+	[[Category: Large Structures]]
	[[Category: Guan, Y]]		[[Category: Guan, Y]]
	[[Category: Hilbers, C W]]		[[Category: Hilbers, C W]]

OCA at 07:02, 29 November 2017

OCA — Wed, 29 Nov 2017 07:02:33 GMT

←Older revision		Revision as of 07:02, 29 November 2017
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		+
	==CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX==		==CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX==
	<StructureSection load='1yha' size='340' side='right' caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1yha' size='340' side='right' caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
-	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://pdbe.org/1yha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha PDBsum]</span></td></tr>	+	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://pdbe.org/1yha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1yha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1yha" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Wang, A H.J]]		[[Category: Wang, A H.J]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]
		+	[[Category: Dna binding protein]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]

OCA at 18:44, 9 February 2016

OCA — Tue, 09 Feb 2016 18:44:07 GMT

←Older revision		Revision as of 18:44, 9 February 2016
Line 15:		Line 15:
	<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=1yha ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:00, 11 September 2015

OCA — Fri, 11 Sep 2015 01:00:39 GMT

←Older revision		Revision as of 01:00, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1yha' size='340' side='right' caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1yha' size='340' side='right' caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_f1 Enterobacteria phage f1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpf1 Bpf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
-	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha PDBsum]</span></td></tr>	+	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://pdbe.org/1yha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~VHED_BPF1 VHED_BPF1~~]] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).	+	[[http://www.uniprot.org/uniprot/G5P_BPF1 G5P_BPF1]] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 25:
	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 1yha" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage f1~~]]	+	[[Category: Bpf1]]
	[[Category: Guan, Y]]		[[Category: Guan, Y]]
	[[Category: Hilbers, C W]]		[[Category: Hilbers, C W]]

OCA at 08:46, 25 December 2014

OCA — Thu, 25 Dec 2014 08:46:25 GMT

←Older revision		Revision as of 08:46, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
-	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha PDBsum]</span></td></tr>	+	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VHED_BPF1 VHED_BPF1]] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage f1]]		[[Category: Enterobacteria phage f1]]
-	[[Category: Guan, Y.]]	+	[[Category: Guan, Y]]
-	[[Category: Hilbers, C W.]]	+	[[Category: Hilbers, C W]]
-	[[Category: Konings, R N.H.]]	+	[[Category: Konings, R N.H]]
-	[[Category: Terwilliger, T C.]]	+	[[Category: Terwilliger, T C]]
-	[[Category: Wang, A H.J.]]	+	[[Category: Wang, A H.J]]
-	[[Category: Zhang, H.]]	+	[[Category: Zhang, H]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]

OCA at 19:58, 29 September 2014

OCA — Mon, 29 Sep 2014 19:58:05 GMT

←Older revision		Revision as of 19:58, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1yha.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX==
		+	<StructureSection load='1yha' size='340' side='right' caption='[[1yha]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHA FirstGlance]. <br>
		+	</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=1yha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yha RCSB], [http://www.ebi.ac.uk/pdbsum/1yha 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/yh/1yha_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 ==
		+	Gene V protein (GVP) encoded by the filamentous phage Ff (M13, fl, fd) is a homodimeric protein of 87 amino acids that binds to single-stranded DNA (ssDNA) nonspecifically and cooperatively. The structure (monoclinic C2 form) of the wild-type protein has been determined and refined at 1.8-A resolution [Skinner et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 2071-2075]. The monomer structure consists of a somewhat distorted five-stranded beta-barrel core with three prominent loops: a DNA-binding loop, a dyad loop, and a dimer contact loop. The amino acid residue at position 41 plays an important role in the dimer-dimer interactions of the protein-ssDNA complex. Two Y41 mutant structures have been studied by X-ray crystallography. The Y41F GVP structure has been refined to an R-factor of 0.180 at 2.2-A resolution and is very similar to the wild-type (wt) structure (rmsd of all C alpha atoms = 0.30 A). In contrast, Y41H GVP forms a new crystal lattice in the space group P2(1)2(1)2(1) with a = 77.18 A, b = 84.17 A, and c = 28.62 A. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-A resolution. The two monomers of Y41H are crystallographically independent, and their structures remain similar to wt-GVP but with significant differences, particularly in the DNA-binding hairpin region. In both crystals, the loop (residues 36-43) that contains the Y41 residue is involved in the crystal dimer packings but in a different manner. The dimer-dimer contacts found in the wt-GVP crystal may be important for GVP aggregation in the absence of DNA. In the presence of DNA, the dimer-dimer contacts may switch to the type found in the Y41H crystal, allowing the GVP-ssDNA complex to form cooperatively. A model of the complex, consistent with existing biochemical and biophysical data, has been constructed from those crystal packing data.

-	~~{{STRUCTURE_1yha\| PDB=1yha \| SCENE= }}~~	+	Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex.,Guan Y, Zhang H, Konings RN, Hilbers CW, Terwilliger TC, Wang AH Biochemistry. 1994 Jun 28;33(25):7768-78. PMID:8011642<ref>PMID:8011642</ref>

-	~~===CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_8011642}}~~	+	==See Also==
-		+	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1yha~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:008011642<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Enterobacteria phage f1]]		[[Category: Enterobacteria phage f1]]
	[[Category: Guan, Y.]]		[[Category: Guan, Y.]]

OCA: Protected "1yha" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:16:39 GMT

Protected "1yha" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:16, 5 January 2013

OCA at 17:16, 5 January 2013

OCA — Sat, 05 Jan 2013 17:16:37 GMT

←Older revision		Revision as of 17:16, 5 January 2013
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-	{{Seed}}
	[[Image:1yha.png\|left\|200px]]		[[Image:1yha.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yha", 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),
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	{{STRUCTURE_1yha\| PDB=1yha \| SCENE= }}		{{STRUCTURE_1yha\| PDB=1yha \| SCENE= }}

	===CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX===		===CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8011642}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8011642 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8011642}}		{{ABSTRACT_PUBMED_8011642}}

	==About this Structure==		==About this Structure==
-	~~1YHA~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA].	+	[[1yha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8011642~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008011642</ref><references group="xtra"/>
	[[Category: Enterobacteria phage f1]]		[[Category: Enterobacteria phage f1]]
	[[Category: Guan, Y.]]		[[Category: Guan, Y.]]
Line 32:		Line 20:
	[[Category: Zhang, H.]]		[[Category: Zhang, H.]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:56:24 2009''