2z4f - Revision history

OCA at 10:45, 8 December 2021

OCA — Wed, 08 Dec 2021 10:45:33 GMT

←Older revision		Revision as of 10:45, 8 December 2021
Line 1:		Line 1:

	==Solution structure of the Discoidin Domain of DDR2==		==Solution structure of the Discoidin Domain of DDR2==
-	<StructureSection load='2z4f' size='340' side='right' caption='[[2z4f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2z4f' size='340' side='right'caption='[[2z4f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [~~http~~://pdbe.org/2z4f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z4f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z4f 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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [https://pdbe.org/2z4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [https://www.ebi.ac.uk/pdbsum/2z4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z4f ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[~~http~~://omim.org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref> <ref>PMID:19110212</ref>	+	[[https://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[https://omim.org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref> <ref>PMID:19110212</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation, remodeling of the extracellular matrix, cell migration and cell proliferation. Required for normal bone development. Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing.<ref>PMID:9659899</ref> <ref>PMID:16186108</ref> <ref>PMID:16186104</ref> <ref>PMID:17665456</ref> <ref>PMID:18201965</ref> <ref>PMID:20564243</ref> <ref>PMID:20734453</ref> <ref>PMID:20004161</ref>	+	[[https://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation, remodeling of the extracellular matrix, cell migration and cell proliferation. Required for normal bone development. Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing.<ref>PMID:9659899</ref> <ref>PMID:16186108</ref> <ref>PMID:16186104</ref> <ref>PMID:17665456</ref> <ref>PMID:18201965</ref> <ref>PMID:20564243</ref> <ref>PMID:20734453</ref> <ref>PMID:20004161</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2z4f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2z4f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Epithelial discoidin domain-containing receptor\|Epithelial discoidin domain-containing receptor]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]
	[[Category: Goshima, N]]		[[Category: Goshima, N]]

OCA at 08:56, 17 October 2018

OCA — Wed, 17 Oct 2018 08:56:48 GMT

←Older revision		Revision as of 08:56, 17 October 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z4/2z4f_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z4/2z4f_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>

OCA at 18:48, 11 August 2016

OCA — Thu, 11 Aug 2016 18:48:04 GMT

←Older revision		Revision as of 18:48, 11 August 2016
Line 1:		Line 1:
		+
	==Solution structure of the Discoidin Domain of DDR2==		==Solution structure of the Discoidin Domain of DDR2==
	<StructureSection load='2z4f' size='340' side='right' caption='[[2z4f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2z4f' size='340' side='right' caption='[[2z4f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [http://www.ebi.ac.uk/pdbsum/2z4f 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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [http://pdbe.org/2z4f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [http://www.ebi.ac.uk/pdbsum/2z4f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z4f ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 19:		Line 20:
	<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=2z4f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2z4f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]
	[[Category: Goshima, N]]		[[Category: Goshima, N]]

OCA at 09:01, 20 January 2015

OCA — Tue, 20 Jan 2015 09:01:18 GMT

←Older revision		Revision as of 09:01, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [http://www.ebi.ac.uk/pdbsum/2z4f 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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [http://www.ebi.ac.uk/pdbsum/2z4f PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[http://omim.org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref> <ref>PMID:19110212</ref>		[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[http://omim.org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref> <ref>PMID:19110212</ref>
Line 35:		Line 35:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]
-	[[Category: Goshima, N.]]	+	[[Category: Goshima, N]]
-	[[Category: Ichikawa, O.]]	+	[[Category: Ichikawa, O]]
-	[[Category: Nishida, N.]]	+	[[Category: Nishida, N]]
-	[[Category: Nomura, N.]]	+	[[Category: Nomura, N]]
-	[[Category: Osawa, M.]]	+	[[Category: Osawa, M]]
-	[[Category: Shimada, I.]]	+	[[Category: Shimada, I]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:20, 2 October 2014

OCA — Thu, 02 Oct 2014 05:20:53 GMT

←Older revision		Revision as of 05:20, 2 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2z4f~~\| ~~PDB~~=2z4f \| ~~SCENE~~= }}	+	==Solution structure of the Discoidin Domain of DDR2==
-	===~~Solution~~ structure of the ~~Discoidin Domain~~ of ~~DDR2~~===	+	<StructureSection load='2z4f' size='340' side='right' caption='[[2z4f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_17703188}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z4F FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></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=2z4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z4f RCSB], [http://www.ebi.ac.uk/pdbsum/2z4f PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[http://omim.org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref> <ref>PMID:19110212</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation, remodeling of the extracellular matrix, cell migration and cell proliferation. Required for normal bone development. Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing.<ref>PMID:9659899</ref> <ref>PMID:16186108</ref> <ref>PMID:16186104</ref> <ref>PMID:17665456</ref> <ref>PMID:18201965</ref> <ref>PMID:20564243</ref> <ref>PMID:20734453</ref> <ref>PMID:20004161</ref>
		+	== 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/z4/2z4f_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 ==
		+	Discoidin domain receptor (DDR) is a cell-surface receptor tyrosine kinase activated by the binding of its discoidin (DS) domain to fibrillar collagen. Here, we have determined the NMR structure of the DS domain in DDR2 (DDR2-DS domain), and identified the binding site to fibrillar collagen by transferred cross-saturation experiments. The DDR2-DS domain structure adopts a distorted jellyroll fold, consisting of eight beta-strands. The collagen-binding site is formed at the interloop trench, consisting of charged residues surrounded by hydrophobic residues. The surface profile of the collagen-binding site suggests that the DDR2-DS domain recognizes specific sites on fibrillar collagen. This study provides a molecular basis for the collagen-binding mode of the DDR2-DS domain.

-	~~==Disease==~~	+	Structural basis of the collagen-binding mode of discoidin domain receptor 2.,Ichikawa O, Osawa M, Nishida N, Goshima N, Nomura N, Shimada I EMBO J. 2007 Sep 19;26(18):4168-76. Epub 2007 Aug 16. PMID:17703188<ref>PMID:17703188</ref>
-	~~[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are~~ the ~~cause~~ of ~~spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[http://omim~~.~~org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism~~, ~~a narrow chest with pectus excavatum~~, ~~brachydactyly in the hands and feet~~, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, ~~flattened and fragmented and flared~~, ~~irregular metaphyses~~. ~~Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear~~-~~shaped with central humps, anterior protrusions and posterior scalloping~~.~~<ref>~~PMID:~~20223752</ref>~~<ref>PMID:~~19110212~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation~~, ~~remodeling~~ of the ~~extracellular matrix, cell migration and cell proliferation~~. ~~Required for normal bone development~~. ~~Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation~~ of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing.<~~ref~~>~~PMID:9659899~~</~~ref~~>~~<ref>PMID:16186108</ref><ref>PMID:16186104</ref><ref>PMID:17665456</ref><ref>PMID:18201965</ref><ref>PMID:20564243</ref><ref>PMID:20734453</ref><ref>PMID:20004161</ref>~~	+	</div>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	~~<ref group="xtra">PMID:017703188</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]

OCA at 04:24, 25 March 2013

OCA — Mon, 25 Mar 2013 04:24:16 GMT

←Older revision		Revision as of 04:24, 25 March 2013
Line 1:		Line 1:
-	[[Image:2z4f.png\|left\|200px]]
-
	{{STRUCTURE_2z4f\| PDB=2z4f \| SCENE= }}		{{STRUCTURE_2z4f\| PDB=2z4f \| SCENE= }}
-
	===Solution structure of the Discoidin Domain of DDR2===		===Solution structure of the Discoidin Domain of DDR2===
		+	{{ABSTRACT_PUBMED_17703188}}

-	~~{{ABSTRACT_PUBMED_17703188}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[http://omim.org/entry/271665 271665]]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref><ref>PMID:19110212</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN]] Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation, remodeling of the extracellular matrix, cell migration and cell proliferation. Required for normal bone development. Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing.<ref>PMID:9659899</ref><ref>PMID:16186108</ref><ref>PMID:16186104</ref><ref>PMID:17665456</ref><ref>PMID:18201965</ref><ref>PMID:20564243</ref><ref>PMID:20734453</ref><ref>PMID:20004161</ref>

	==About this Structure==		==About this Structure==
Line 11:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:017703188</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017703188</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]

OCA: Protected "2z4f" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 21:19:37 GMT

Protected "2z4f" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:19, 7 January 2013

OCA at 21:19, 7 January 2013

OCA — Mon, 07 Jan 2013 21:19:33 GMT

←Older revision		Revision as of 21:19, 7 January 2013
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-	{{Seed}}
	[[Image:2z4f.png\|left\|200px]]		[[Image:2z4f.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z4f", 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_2z4f\| PDB=2z4f \| SCENE= }}		{{STRUCTURE_2z4f\| PDB=2z4f \| SCENE= }}

	===Solution structure of the Discoidin Domain of DDR2===		===Solution structure of the Discoidin Domain of DDR2===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17703188}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17703188 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17703188}}		{{ABSTRACT_PUBMED_17703188}}

	==About this Structure==		==About this Structure==
-	~~2Z4F~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].	+	[[2z4f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17703188~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017703188</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]
Line 34:		Line 22:
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:05:17 2009''

OCA at 06:05, 18 February 2009

OCA — Wed, 18 Feb 2009 06:05:20 GMT

←Older revision		Revision as of 06:05, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z4F is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].	+	2Z4F is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].

	==Reference==		==Reference==
-	~~Structural basis of the collagen-binding mode of discoidin domain receptor 2., Ichikawa O, Osawa M, Nishida N, Goshima N, Nomura N, Shimada I, EMBO J. 2007 Sep 19;26(18):4168-76. Epub 2007 Aug 16.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17703188 17703188]~~	+	<ref group="xtra">PMID:17703188</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]
-	[[Category: Single protein]]
	[[Category: Goshima, N.]]		[[Category: Goshima, N.]]
	[[Category: Ichikawa, O.]]		[[Category: Ichikawa, O.]]
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	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 14~~:33:~~14 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:05:17 2009''

OCA at 11:33, 29 July 2008

OCA — Tue, 29 Jul 2008 11:33:21 GMT

←Older revision		Revision as of 11:33, 29 July 2008
Line 1:		Line 1:
-	[[Image:2z4f.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2z4f.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2z4f\| PDB=2z4f \| SCENE= }}		{{STRUCTURE_2z4f\| PDB=2z4f \| SCENE= }}

-	~~'''~~Solution structure of the Discoidin Domain of DDR2~~'''~~	+	===Solution structure of the Discoidin Domain of DDR2===


-	~~==Overview==~~	+	<!--
-	~~Discoidin domain receptor (DDR) is a cell-surface receptor tyrosine kinase activated by~~ the ~~binding of its discoidin (DS) domain~~ to ~~fibrillar collagen. Here, we have determined~~ the ~~NMR structure of the DS domain in DDR2~~ (~~DDR2-DS domain~~), and identified the binding site to fibrillar collagen by transferred cross-saturation experiments. The DDR2-DS domain structure adopts a distorted jellyroll fold, consisting of eight beta-strands. The collagen-binding site is ~~formed at~~ the ~~interloop trench, consisting of charged residues surrounded by hydrophobic residues~~. ~~The surface profile of the collagen~~-~~binding site suggests that the DDR2~~-~~DS domain recognizes specific sites on fibrillar collagen. This study provides a molecular basis for the collagen-binding mode of the DDR2-DS domain.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17703188}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17703188 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17703188}}

	==About this Structure==		==About this Structure==
-	2Z4F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].	+	2Z4F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z4F OCA].

	==Reference==		==Reference==
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	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 19~~:56:24 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:33:14 2008''