3ioz - Revision history

OCA at 10:06, 21 February 2024

2024-02-21T10:06:13Z

←Older revision		Revision as of 10:06, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3ioz' size='340' side='right'caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>		<StructureSection load='3ioz' size='340' side='right'caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~] and [https://en.wikipedia.org/wiki/~~Siv_~~-_cpz ~~Siv~~ - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Simian_immunodeficiency_virus_-_cpz Simian immunodeficiency virus - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~3ik5~~\|~~3ik5~~]]~~</div>~~</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]] 3.699Å</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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [https://pdbe.org/3ioz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [https://www.ebi.ac.uk/pdbsum/3ioz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ioz 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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [https://pdbe.org/3ioz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [https://www.ebi.ac.uk/pdbsum/3ioz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ioz ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[https://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[https://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~CD3Z_HUMAN CD3Z_HUMAN~~]~~] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.~~	+	[https://www.uniprot.org/uniprot/Q5QGG3_SIV Q5QGG3_SIV]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 19:
	</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=3ioz 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=3ioz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning.
-
-	Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.,Kim WM, Sigalov AB, Stern LJ Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):163-75. Epub 2010 Jan 22. PMID:20124696<ref>PMID:20124696</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3ioz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[CD3 3D structures\|CD3 3D structures]]		*[[CD3 3D structures\|CD3 3D structures]]
-	*[[Protein Nef\|Protein Nef]]	+	*[[Protein Nef 3D structures\|Protein Nef 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Siv~~ - cpz]]	+	[[Category: Simian immunodeficiency virus - cpz]]
-	[[Category: Kim~~, W M~~]]	+	[[Category: Kim WM]]
-	[[Category: Sigalov~~, A B~~]]	+	[[Category: Sigalov AB]]
-	[[Category: Stern~~, L J]]~~	+	[[Category: Stern LJ]]
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Host-virus interaction]]~~	+
-	~~[[Category: Lipoprotein]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Myristate]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Protein-protein complex]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Viral immunoevasion]]~~	+
-	~~[[Category: Viral protein-antiviral protein complex]]~~	+
-	~~[[Category: Viral protein-signaling protein complex]]~~	+
-	~~[[Category: Virulence~~]]	+

OCA at 03:37, 21 April 2022

2022-04-21T03:37:58Z

←Older revision		Revision as of 03:37, 21 April 2022
Line 3:		Line 3:
	<StructureSection load='3ioz' size='340' side='right'caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>		<StructureSection load='3ioz' size='340' side='right'caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human] and [~~http~~://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ik5\|3ik5]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ik5\|3ik5]]</div></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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [~~http~~://pdbe.org/3ioz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ioz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ioz 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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [https://pdbe.org/3ioz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [https://www.ebi.ac.uk/pdbsum/3ioz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ioz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[~~http~~://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref>	+	[[https://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[https://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.	+	[[https://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:11, 7 August 2019

2019-08-07T07:11:47Z

←Older revision		Revision as of 07:11, 7 August 2019
Line 1:		Line 1:

	==SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)==		==SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)==
-	<StructureSection load='3ioz' size='340' side='right' caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>	+	<StructureSection load='3ioz' size='340' side='right'caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/3ioz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/3ioz_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 32:		Line 32:

	==See Also==		==See Also==
-	*[[CD3\|CD3]]	+	*[[CD3 3D structures\|CD3 3D structures]]
		+	*[[Protein Nef\|Protein Nef]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Siv - cpz]]		[[Category: Siv - cpz]]
	[[Category: Kim, W M]]		[[Category: Kim, W M]]

OCA at 08:11, 1 November 2017

2017-11-01T08:11:09Z

←Older revision		Revision as of 08:11, 1 November 2017
Line 1:		Line 1:
		+
	==SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)==		==SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)==
	<StructureSection load='3ioz' size='340' side='right' caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>		<StructureSection load='3ioz' size='340' side='right' caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ik5\|3ik5]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ik5\|3ik5]]</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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [http://pdbe.org/3ioz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [http://www.ebi.ac.uk/pdbsum/3ioz 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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [http://pdbe.org/3ioz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [http://www.ebi.ac.uk/pdbsum/3ioz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ioz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 03:11, 8 February 2016

2016-02-08T03:11:19Z

←Older revision		Revision as of 03:11, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3ioz' size='340' side='right' caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>		<StructureSection load='3ioz' size='340' side='right' caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/~~Simian_immunodeficiency_virus Simian immunodeficiency virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ik5\|3ik5]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ik5\|3ik5]]</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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [http://www.ebi.ac.uk/pdbsum/3ioz 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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [http://pdbe.org/3ioz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [http://www.ebi.ac.uk/pdbsum/3ioz PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 18:		Line 18:
	<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=3ioz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3ioz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
-	[[Category: ~~Simian immunodeficiency virus~~]]	+	[[Category: Siv - cpz]]
	[[Category: Kim, W M]]		[[Category: Kim, W M]]
	[[Category: Sigalov, A B]]		[[Category: Sigalov, A B]]

OCA at 15:31, 18 December 2014

2014-12-18T15:31:17Z

←Older revision		Revision as of 15:31, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3ioz\| PDB=3ioz \| SCENE= }}~~	+	==SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)==
-	===SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)===	+	<StructureSection load='3ioz' size='340' side='right' caption='[[3ioz]], [[Resolution\|resolution]] 3.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20124696}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IOZ FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ik5\|3ik5]]</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=3ioz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ioz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ioz RCSB], [http://www.ebi.ac.uk/pdbsum/3ioz PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[http://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.
		+	== 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/io/3ioz_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 ==
		+	HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning.

-	~~==Disease==~~	+	Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.,Kim WM, Sigalov AB, Stern LJ Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):163-75. Epub 2010 Jan 22. PMID:20124696<ref>PMID:20124696</ref>
-	~~[[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects~~ in ~~CD247 are the cause~~ of ~~immunodeficiency due~~ to ~~defect in CD3~~-~~zeta~~ (~~CD3ZID~~) ~~[MIM~~:~~[http://omim~~.~~org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens~~.<ref>PMID:~~16672702~~</ref>	+
-		+
-	~~==Function==~~	+
-	~~[[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3ioz]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] and [http://en~~.~~wikipedia.org~~/~~wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:020124696</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[CD3\|CD3]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Simian immunodeficiency virus]]		[[Category: Simian immunodeficiency virus]]
-	[[Category: Kim, W M.]]	+	[[Category: Kim, W M]]
-	[[Category: Sigalov, A B.]]	+	[[Category: Sigalov, A B]]
-	[[Category: Stern, L J.]]	+	[[Category: Stern, L J]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]

OCA at 03:56, 25 March 2013

2013-03-25T03:56:03Z

←Older revision		Revision as of 03:56, 25 March 2013
Line 1:		Line 1:
-	[[Image:3ioz.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ioz", 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_3ioz\| PDB=3ioz \| SCENE= }}		{{STRUCTURE_3ioz\| PDB=3ioz \| SCENE= }}
-
	===SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)===		===SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)===
		+	{{ABSTRACT_PUBMED_20124696}}

		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[http://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref>

-	~~<!--~~	+	==Function==
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20124696}}, adds the Publication Abstract to the page~~	+	[[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 20124696 is~~ the ~~PubMed ID number~~.	+
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_20124696}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:020124696</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020124696</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Simian immunodeficiency virus]]		[[Category: Simian immunodeficiency virus]]

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

2012-03-28T06:45:58Z

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

←Older revision

Revision as of 06:45, 28 March 2012

OCA at 06:45, 28 March 2012

2012-03-28T06:45:56Z

←Older revision		Revision as of 06:45, 28 March 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3ioz.png\|left\|200px]]
-	[[Image:3ioz.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 12:		Line 11:
	===SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)===		===SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20124696}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20124696 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20124696}}

	==About this Structure==		==About this Structure==
-	~~3IOZ~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA].	+	[[3ioz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:020124696</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Simian immunodeficiency virus]]		[[Category: Simian immunodeficiency virus]]
Line 20:		Line 28:
	[[Category: Sigalov, A B.]]		[[Category: Sigalov, A B.]]
	[[Category: Stern, L J.]]		[[Category: Stern, L J.]]
-	[[Category: Alternative splicing]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]
Line 32:		Line 39:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Viral immunoevasion]]		[[Category: Viral immunoevasion]]
-	[[Category: Viral protein/antiviral protein complex]]	+	[[Category: Viral protein-antiviral protein complex]]
-	[[Category: Viral protein/signaling protein complex]]	+	[[Category: Viral protein-signaling protein complex]]
	[[Category: Virulence]]		[[Category: Virulence]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:55:30 2010''

OCA at 07:55, 3 February 2010

2010-02-03T07:55:31Z

←Older revision		Revision as of 07:55, 3 February 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3ioz.jpg\|left\|200px]]

-	The ~~entry 3ioz~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ioz", 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_3ioz\| PDB=3ioz \| SCENE= }}

-	~~Authors: Kim, W.M., Sigalov, A.B., Stern, L.J.~~	+	===SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)===

-	Description: SIVmac239 Nef in complex with a TCR zeta ITAM 1 polypeptide (L51-D93)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 21~~ 09:59:~~10 2009~~''	+	==About this Structure==
		+	3IOZ is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Simian_immunodeficiency_virus Simian immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOZ OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Simian immunodeficiency virus]]
		+	[[Category: Kim, W M.]]
		+	[[Category: Sigalov, A B.]]
		+	[[Category: Stern, L J.]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Cell membrane]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Host-virus interaction]]
		+	[[Category: Lipoprotein]]
		+	[[Category: Membrane]]
		+	[[Category: Myristate]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Protein-protein complex]]
		+	[[Category: Receptor]]
		+	[[Category: Transmembrane]]
		+	[[Category: Viral immunoevasion]]
		+	[[Category: Viral protein/antiviral protein complex]]
		+	[[Category: Viral protein/signaling protein complex]]
		+	[[Category: Virulence]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:55:30 2010''