5e6w - Revision history

OCA at 06:15, 5 July 2023

OCA — Wed, 05 Jul 2023 06:15:09 GMT

←Older revision		Revision as of 06:15, 5 July 2023
Line 3:		Line 3:
	<StructureSection load='5e6w' size='340' side='right'caption='[[5e6w]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5e6w' size='340' side='right'caption='[[5e6w]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e6w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E6W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e6w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E6W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NAG:N~~-~~ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[2p28\|2p28]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ITGB2, CD18, MFI7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [https://pdbe.org/5e6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [https://www.ebi.ac.uk/pdbsum/5e6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e6w ProSAT]</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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [~~http~~://pdbe.org/5e6w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e6w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e6w ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN]] Defects in ITGB2 are the cause of leukocyte adhesion deficiency type 1 (LAD1) [MIM:[~~http~~://omim.org/entry/116920 116920]]. LAD1 patients have recurrent bacterial infections and their leukocytes are deficient in a wide range of adhesion-dependent functions.<ref>PMID:7509236</ref> <ref>PMID:1346613</ref> <ref>PMID:1968911</ref> <ref>PMID:1694220</ref> <ref>PMID:1590804</ref> <ref>PMID:1352501</ref> <ref>PMID:1347532</ref> <ref>PMID:7686755</ref> <ref>PMID:9884339</ref> <ref>PMID:20529581</ref> <ref>PMID:20549317</ref>	+	[https://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN] Defects in ITGB2 are the cause of leukocyte adhesion deficiency type 1 (LAD1) [MIM:[https://omim.org/entry/116920 116920]. LAD1 patients have recurrent bacterial infections and their leukocytes are deficient in a wide range of adhesion-dependent functions.<ref>PMID:7509236</ref> <ref>PMID:1346613</ref> <ref>PMID:1968911</ref> <ref>PMID:1694220</ref> <ref>PMID:1590804</ref> <ref>PMID:1352501</ref> <ref>PMID:1347532</ref> <ref>PMID:7686755</ref> <ref>PMID:9884339</ref> <ref>PMID:20529581</ref> <ref>PMID:20549317</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN]] Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrins alpha-M/beta-2 and alpha-X/beta-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen. Integrin alpha-X/beta-2 recognizes the sequence G-P-R in fibrinogen alpha-chain. Integrin alpha-M/beta-2 recognizes P1 and P2 peptides of fibrinogen gamma chain. Integrin alpha-M/beta-2 is also a receptor for factor X. Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. Triggers neutrophil transmigration during lung injury through PTK2B/PYK2-mediated activation.<ref>PMID:18587400</ref>	+	[https://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN] Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrins alpha-M/beta-2 and alpha-X/beta-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen. Integrin alpha-X/beta-2 recognizes the sequence G-P-R in fibrinogen alpha-chain. Integrin alpha-M/beta-2 recognizes P1 and P2 peptides of fibrinogen gamma chain. Integrin alpha-M/beta-2 is also a receptor for factor X. Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. Triggers neutrophil transmigration during lung injury through PTK2B/PYK2-mediated activation.<ref>PMID:18587400</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Integrins mediate cell adhesion in response to activation signals that trigger conformational changes within their ectodomain. It is thought that a compact bent conformation~~ of the ~~molecule represents its physiological low affinity state and extended conformations its active state. We have determined the structure~~ of ~~two integrin fragments of the beta2 subunit. The first structure, consisting of the plexin~~-~~semaphorin~~-~~integrin domain, hybrid, integrin-epidermal growth factor~~ 1 (~~I-EGF1~~)~~, and I-EGF2 domains (PHE2), showed an L-shaped conformation~~ with the ~~bend located between the I~~-~~EGF1~~ and I-~~EGF2~~ domains. The ~~second structure, which includes, in addition,~~ the ~~I-EGF3~~ domain, ~~showed an extended conformation. The major reorientation of I~~-~~EGF2 with respect~~ to the ~~other domains in~~ the ~~two~~ structures is ~~accompanied~~ by a ~~change of torsion angle of~~ the ~~disulfide bond~~ between ~~Cys(461)~~-~~Cys(492) by 180 degrees~~ and ~~the conversion of a short alpha-helix (residues Ser(468)-Cys(475)) into a flexible coil~~. ~~Based on the PHE2 structure, we introduced a disulfide bond~~ between the ~~plexin-semaphorin-integrin domain~~ and I-~~EGF2~~ domains in the ~~beta2 subunit~~. ~~The resultant alphaLbeta2 integrin (leukocyte function-associated antigen-1) variant was locked~~ in ~~a bent state and could not be detected with~~ the ~~monoclonal antibody KIM127 in Mg~~(2+)~~/EGTA. However, it retained~~ the binding ~~activity to ICAM-1. These results provide a structural hypothesis~~ for ~~our understanding of~~ the ~~transition between the resting and active states of leukocyte function-associated antigen-1~~.	+	High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin alphaLbeta2) reveal how the alphaI domain interacts with its platform formed by the alpha-subunit beta-propeller and beta-subunit betaI domains. The alphaLbeta2 structures compared with alphaXbeta2 structures show that the alphaI domain, tethered through its N-linker and a disulfide to a stable beta-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between alphaL and alphaX subunits. Rerefined beta2 integrin structures reveal details including pyroglutamic acid at the beta2 N terminus and bending within the EGF1 domain. Allostery is relayed to the alphaI domain by an internal ligand that binds to a pocket at the interface between the beta-propeller and betaI domains. Marked differences between the alphaL and alphaX subunit beta-propeller domains concentrate near the binding pocket and alphaI domain interfaces. Remarkably, movement in allostery in the betaI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.

-	~~A structural hypothesis~~ for the ~~transition between bent~~ and ~~extended conformations~~ of ~~the leukocyte beta2 integrins~~.,~~Shi~~ M, ~~Foo SY, Tan SM, Mitchell EP, Law SK, Lescar J J Biol Chem~~. ~~2007 Oct 12~~;~~282~~(41):~~30198~~-~~206~~. Epub ~~2007 Aug 1~~. PMID:~~17673459~~<ref>PMID:~~17673459~~</ref>	+	Leukocyte integrin alphaLbeta2 headpiece structures: The alphaI domain, the pocket for the internal ligand, and concerted movements of its loops.,Sen M, Springer TA Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2940-5. doi:, 10.1073/pnas.1601379113. Epub 2016 Mar 2. PMID:26936951<ref>PMID:26936951</ref>

	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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sen, M]]	+	[[Category: Sen M]]
-	[[Category: Springer~~, T A]]~~	+	[[Category: Springer TA]]
-	~~[[Category: Cd18 fragment]]~~	+
-	~~[[Category: Cell adhesion~~]]	+

OCA at 08:59, 4 December 2019

OCA — Wed, 04 Dec 2019 08:59:57 GMT

←Older revision		Revision as of 08:59, 4 December 2019
Line 1:		Line 1:

	==Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit==		==Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit==
-	<StructureSection load='5e6w' size='340' side='right' caption='[[5e6w]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5e6w' size='340' side='right'caption='[[5e6w]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E6W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p28\|2p28]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p28\|2p28]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ITGB2, CD18, MFI7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [http://pdbe.org/5e6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [http://www.ebi.ac.uk/pdbsum/5e6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e6w ProSAT]</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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [http://pdbe.org/5e6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [http://www.ebi.ac.uk/pdbsum/5e6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e6w ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5e6w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5e6w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Integrin 3D structures\|Integrin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Sen, M]]		[[Category: Sen, M]]
	[[Category: Springer, T A]]		[[Category: Springer, T A]]
	[[Category: Cd18 fragment]]		[[Category: Cd18 fragment]]
	[[Category: Cell adhesion]]		[[Category: Cell adhesion]]

OCA at 13:30, 15 March 2017

OCA — Wed, 15 Mar 2017 13:30:01 GMT

←Older revision		Revision as of 13:30, 15 March 2017
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p28\|2p28]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p28\|2p28]]</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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [http://pdbe.org/5e6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [http://www.ebi.ac.uk/pdbsum/5e6w 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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [http://pdbe.org/5e6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [http://www.ebi.ac.uk/pdbsum/5e6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e6w ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 14:		Line 14:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~High-resolution crystal structures~~ of the ~~headpiece~~ of ~~lymphocyte function~~-~~associated antigen~~-1 (~~integrin alphaLbeta2~~) ~~reveal how the alphaI domain interacts~~ with ~~its platform formed by~~ the ~~alpha~~-~~subunit beta-propeller~~ and ~~beta~~-~~subunit betaI~~ domains. The ~~alphaLbeta2 structures compared with alphaXbeta2 structures show that~~ the ~~alphaI~~ domain, ~~tethered through its N~~-~~linker and a disulfide~~ to ~~a stable beta-ribbon pillar near~~ the ~~center of~~ the ~~platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between alphaL and alphaX subunits. Rerefined beta2 integrin~~ structures ~~reveal details including pyroglutamic acid at the beta2 N terminus and bending within the EGF1 domain. Allostery~~ is ~~relayed to the alphaI domain~~ by ~~an internal ligand that binds to~~ a ~~pocket at~~ the ~~interface~~ between ~~the beta~~-~~propeller~~ and ~~betaI domains~~. ~~Marked differences~~ between the ~~alphaL~~ and ~~alphaX subunit beta~~-~~propeller~~ domains ~~concentrate near~~ the ~~binding pocket and alphaI domain interfaces~~. ~~Remarkably, movement in allostery~~ in the ~~betaI domain of specificity determining loop 1~~ (~~SDL1~~) ~~causes concerted movement of SDL2 and thereby tightens~~ the binding ~~pocket~~ for the ~~internal ligand~~.	+	Integrins mediate cell adhesion in response to activation signals that trigger conformational changes within their ectodomain. It is thought that a compact bent conformation of the molecule represents its physiological low affinity state and extended conformations its active state. We have determined the structure of two integrin fragments of the beta2 subunit. The first structure, consisting of the plexin-semaphorin-integrin domain, hybrid, integrin-epidermal growth factor 1 (I-EGF1), and I-EGF2 domains (PHE2), showed an L-shaped conformation with the bend located between the I-EGF1 and I-EGF2 domains. The second structure, which includes, in addition, the I-EGF3 domain, showed an extended conformation. The major reorientation of I-EGF2 with respect to the other domains in the two structures is accompanied by a change of torsion angle of the disulfide bond between Cys(461)-Cys(492) by 180 degrees and the conversion of a short alpha-helix (residues Ser(468)-Cys(475)) into a flexible coil. Based on the PHE2 structure, we introduced a disulfide bond between the plexin-semaphorin-integrin domain and I-EGF2 domains in the beta2 subunit. The resultant alphaLbeta2 integrin (leukocyte function-associated antigen-1) variant was locked in a bent state and could not be detected with the monoclonal antibody KIM127 in Mg(2+)/EGTA. However, it retained the binding activity to ICAM-1. These results provide a structural hypothesis for our understanding of the transition between the resting and active states of leukocyte function-associated antigen-1.

-	~~Leukocyte integrin alphaLbeta2 headpiece structures: The alphaI domain, the pocket~~ for the ~~internal ligand,~~ and ~~concerted movements~~ of ~~its loops~~.,~~Sen~~ M, ~~Springer TA Proc Natl Acad Sci U S A~~. ~~2016 Mar 15~~;~~113~~(11):~~2940~~-~~5. doi:, 10.1073/pnas.1601379113~~. Epub ~~2016 Mar 2~~. PMID:~~26936951~~<ref>PMID:~~26936951~~</ref>	+	A structural hypothesis for the transition between bent and extended conformations of the leukocyte beta2 integrins.,Shi M, Foo SY, Tan SM, Mitchell EP, Law SK, Lescar J J Biol Chem. 2007 Oct 12;282(41):30198-206. Epub 2007 Aug 1. PMID:17673459<ref>PMID:17673459</ref>

	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>

OCA at 19:34, 10 May 2016

OCA — Tue, 10 May 2016 19:34:02 GMT

←Older revision		Revision as of 19:34, 10 May 2016
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN]] Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrins alpha-M/beta-2 and alpha-X/beta-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen. Integrin alpha-X/beta-2 recognizes the sequence G-P-R in fibrinogen alpha-chain. Integrin alpha-M/beta-2 recognizes P1 and P2 peptides of fibrinogen gamma chain. Integrin alpha-M/beta-2 is also a receptor for factor X. Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. Triggers neutrophil transmigration during lung injury through PTK2B/PYK2-mediated activation.<ref>PMID:18587400</ref>		[[http://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN]] Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrins alpha-M/beta-2 and alpha-X/beta-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen. Integrin alpha-X/beta-2 recognizes the sequence G-P-R in fibrinogen alpha-chain. Integrin alpha-M/beta-2 recognizes P1 and P2 peptides of fibrinogen gamma chain. Integrin alpha-M/beta-2 is also a receptor for factor X. Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. Triggers neutrophil transmigration during lung injury through PTK2B/PYK2-mediated activation.<ref>PMID:18587400</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin alphaLbeta2) reveal how the alphaI domain interacts with its platform formed by the alpha-subunit beta-propeller and beta-subunit betaI domains. The alphaLbeta2 structures compared with alphaXbeta2 structures show that the alphaI domain, tethered through its N-linker and a disulfide to a stable beta-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between alphaL and alphaX subunits. Rerefined beta2 integrin structures reveal details including pyroglutamic acid at the beta2 N terminus and bending within the EGF1 domain. Allostery is relayed to the alphaI domain by an internal ligand that binds to a pocket at the interface between the beta-propeller and betaI domains. Marked differences between the alphaL and alphaX subunit beta-propeller domains concentrate near the binding pocket and alphaI domain interfaces. Remarkably, movement in allostery in the betaI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.
		+
		+	Leukocyte integrin alphaLbeta2 headpiece structures: The alphaI domain, the pocket for the internal ligand, and concerted movements of its loops.,Sen M, Springer TA Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2940-5. doi:, 10.1073/pnas.1601379113. Epub 2016 Mar 2. PMID:26936951<ref>PMID:26936951</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5e6w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:24, 2 March 2016

OCA — Wed, 02 Mar 2016 15:24:45 GMT

←Older revision		Revision as of 15:24, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5e6w is ON HOLD~~	+	==Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit==
-		+	<StructureSection load='5e6w' size='340' side='right' caption='[[5e6w]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors: Springer, T.A., Sen, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5e6w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E6W FirstGlance]. <br>
-	~~Description:~~ Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p28\|2p28]]</td></tr>
-	[[~~Category~~: ~~Springer~~, T.A]]	+	<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=5e6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e6w OCA], [http://pdbe.org/5e6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e6w RCSB], [http://www.ebi.ac.uk/pdbsum/5e6w PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN]] Defects in ITGB2 are the cause of leukocyte adhesion deficiency type 1 (LAD1) [MIM:[http://omim.org/entry/116920 116920]]. LAD1 patients have recurrent bacterial infections and their leukocytes are deficient in a wide range of adhesion-dependent functions.<ref>PMID:7509236</ref> <ref>PMID:1346613</ref> <ref>PMID:1968911</ref> <ref>PMID:1694220</ref> <ref>PMID:1590804</ref> <ref>PMID:1352501</ref> <ref>PMID:1347532</ref> <ref>PMID:7686755</ref> <ref>PMID:9884339</ref> <ref>PMID:20529581</ref> <ref>PMID:20549317</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ITB2_HUMAN ITB2_HUMAN]] Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrins alpha-M/beta-2 and alpha-X/beta-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen. Integrin alpha-X/beta-2 recognizes the sequence G-P-R in fibrinogen alpha-chain. Integrin alpha-M/beta-2 recognizes P1 and P2 peptides of fibrinogen gamma chain. Integrin alpha-M/beta-2 is also a receptor for factor X. Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. Triggers neutrophil transmigration during lung injury through PTK2B/PYK2-mediated activation.<ref>PMID:18587400</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Sen, M]]		[[Category: Sen, M]]
		+	[[Category: Springer, T A]]
		+	[[Category: Cd18 fragment]]
		+	[[Category: Cell adhesion]]

OCA at 11:41, 16 December 2015

OCA — Wed, 16 Dec 2015 11:41:02 GMT

←Older revision		Revision as of 11:41, 16 December 2015
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	Description: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit		Description: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sen, M]]
	[[Category: Springer, T.A]]		[[Category: Springer, T.A]]
		+	[[Category: Sen, M]]

OCA at 11:38, 9 December 2015

OCA — Wed, 09 Dec 2015 11:38:01 GMT

←Older revision		Revision as of 11:38, 9 December 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e6w is ON HOLD ~~until sometime in the future~~	+	The entry 5e6w is ON HOLD

	Authors: Springer, T.A., Sen, M.		Authors: Springer, T.A., Sen, M.

OCA at 02:28, 1 December 2015

OCA — Tue, 01 Dec 2015 02:28:21 GMT

←Older revision		Revision as of 02:28, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e6w is ON HOLD	+	The entry 5e6w is ON HOLD until sometime in the future

	Authors: Springer, T.A., Sen, M.		Authors: Springer, T.A., Sen, M.

OCA: Protected "5e6w" [edit=sysop:move=sysop]

OCA — Thu, 22 Oct 2015 04:25:30 GMT

Protected "5e6w" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 22 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e6w is ON HOLD Authors: Springer, T.A., Sen, M. Description: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybri...

OCA — Thu, 22 Oct 2015 04:25:29 GMT

New page: '''Unreleased structure''' The entry 5e6w is ON HOLD Authors: Springer, T.A., Sen, M. Description: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybri...

New page

'''Unreleased structure'''

The entry 5e6w is ON HOLD

Authors: Springer, T.A., Sen, M.

Description: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit
[[Category: Unreleased Structures]]
[[Category: Sen, M]]
[[Category: Springer, T.A]]