3rzw - Revision history

OCA at 09:46, 1 March 2024

OCA — Fri, 01 Mar 2024 09:46:33 GMT

←Older revision		Revision as of 09:46, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3rzw' size='340' side='right'caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3rzw' size='340' side='right'caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rzw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rzw]] is a 4 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=3RZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3uyo\|3uyo]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 ([https://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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [https://pdbe.org/3rzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [https://www.ebi.ac.uk/pdbsum/3rzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rzw 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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [https://pdbe.org/3rzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [https://www.ebi.ac.uk/pdbsum/3rzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rzw ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[https://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref>	+	[https://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[https://omim.org/entry/613705 613705]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref> <ref>PMID:9162015</ref> <ref>PMID:18538659</ref> <ref>PMID:18408734</ref>	+	[https://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref> <ref>PMID:9162015</ref> <ref>PMID:18538659</ref> <ref>PMID:18408734</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The fibronectin type III domain (FN3) has become one of the most widely used non-antibody scaffolds for generating new binding proteins. Because of its structural homology to the immunoglobulin domain, combinatorial libraries of FN3 designed to date have primarily focused on introducing amino acid diversity into three loops that are equivalent to antibody complementarity-determining regions. Here, we report an FN3 library that utilizes alternative positions for presenting amino acid diversity. We diversified positions on a beta-sheet and surface loops that together form a concave surface. The new library produced binding proteins (termed "monobodies") to multiple target proteins, generally with similar efficacy as the original, loop-focused library. The crystal structure of a monobody generated from the new library in complex with its target, the Abl SH2 domain, revealed that a concave surface of the monobody, as intended in our design, bound to a convex surface of the target with the interface area being among the largest of published structures of monobody-target complexes. This mode of interaction differs from a common binding mode for single-domain antibodies and antibody mimics in which recognition loops recognize clefts in targets. Together, this work illustrates the utilization of different surfaces of a single immunoglobulin-like scaffold to generate binding proteins with distinct characteristics.	+
-		+
-	Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.,Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S J Mol Biol. 2012 Jan 13;415(2):393-405. Epub 2011 Dec 16. PMID:22198408<ref>PMID:22198408</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rzw" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 29:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gilbreth~~, R N~~]]	+	[[Category: Gilbreth RN]]
-	[[Category: Koide, S]]	+	[[Category: Koide S]]
-	~~[[Category: Antibody mimic]]~~	+
-	~~[[Category: Beta grasp]]~~	+
-	~~[[Category: Beta sandwich]]~~	+
-	~~[[Category: Engineered binding protein]]~~	+
-	~~[[Category: Post-translational modification]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 10:32, 22 June 2022

OCA — Wed, 22 Jun 2022 10:32:04 GMT

←Older revision		Revision as of 10:32, 22 June 2022
Line 1:		Line 1:

	==Crystal Structure of the Monobody ySMB-9 bound to human SUMO1==		==Crystal Structure of the Monobody ySMB-9 bound to human SUMO1==
-	<StructureSection load='3rzw' size='340' side='right' caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='3rzw' size='340' side='right'caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rzw]] is a 4 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=3RZW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rzw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uyo\|3uyo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3uyo\|3uyo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 ([https://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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [~~http~~://pdbe.org/3rzw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rzw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rzw 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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [https://pdbe.org/3rzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [https://www.ebi.ac.uk/pdbsum/3rzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rzw ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[~~http~~://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref>	+	[[https://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[https://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref> <ref>PMID:9162015</ref> <ref>PMID:18538659</ref> <ref>PMID:18408734</ref>	+	[[https://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref> <ref>PMID:9162015</ref> <ref>PMID:18538659</ref> <ref>PMID:18408734</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 3rzw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3rzw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[SUMO 3D Structures\|SUMO 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gilbreth, R N]]		[[Category: Gilbreth, R N]]
	[[Category: Koide, S]]		[[Category: Koide, S]]

OCA at 09:31, 8 November 2017

OCA — Wed, 08 Nov 2017 09:31:32 GMT

←Older revision		Revision as of 09:31, 8 November 2017
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 3rzw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3rzw" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[SUMO\|SUMO]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:35, 5 August 2016

OCA — Fri, 05 Aug 2016 23:35:02 GMT

←Older revision		Revision as of 23:35, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Monobody ySMB-9 bound to human SUMO1==		==Crystal Structure of the Monobody ySMB-9 bound to human SUMO1==
	<StructureSection load='3rzw' size='340' side='right' caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3rzw' size='340' side='right' caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rzw]] is a 4 chain structure with 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=3RZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rzw]] is a 4 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=3RZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uyo\|3uyo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uyo\|3uyo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 ([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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [http://www.ebi.ac.uk/pdbsum/3rzw 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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [http://pdbe.org/3rzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [http://www.ebi.ac.uk/pdbsum/3rzw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rzw ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	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 3rzw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[SUMO\|SUMO]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Gilbreth, R N]]		[[Category: Gilbreth, R N]]
	[[Category: Koide, S]]		[[Category: Koide, S]]

OCA at 11:12, 19 December 2014

OCA — Fri, 19 Dec 2014 11:12:01 GMT

←Older revision		Revision as of 11:12, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3rzw\| PDB=3rzw \| SCENE= }}~~	+	==Crystal Structure of the Monobody ySMB-9 bound to human SUMO1==
-	===Crystal Structure of the Monobody ySMB-9 bound to human SUMO1===	+	<StructureSection load='3rzw' size='340' side='right' caption='[[3rzw]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22198408}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rzw]] is a 4 chain structure with 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=3RZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uyo\|3uyo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3rzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rzw RCSB], [http://www.ebi.ac.uk/pdbsum/3rzw PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[http://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref> <ref>PMID:9162015</ref> <ref>PMID:18538659</ref> <ref>PMID:18408734</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The fibronectin type III domain (FN3) has become one of the most widely used non-antibody scaffolds for generating new binding proteins. Because of its structural homology to the immunoglobulin domain, combinatorial libraries of FN3 designed to date have primarily focused on introducing amino acid diversity into three loops that are equivalent to antibody complementarity-determining regions. Here, we report an FN3 library that utilizes alternative positions for presenting amino acid diversity. We diversified positions on a beta-sheet and surface loops that together form a concave surface. The new library produced binding proteins (termed "monobodies") to multiple target proteins, generally with similar efficacy as the original, loop-focused library. The crystal structure of a monobody generated from the new library in complex with its target, the Abl SH2 domain, revealed that a concave surface of the monobody, as intended in our design, bound to a convex surface of the target with the interface area being among the largest of published structures of monobody-target complexes. This mode of interaction differs from a common binding mode for single-domain antibodies and antibody mimics in which recognition loops recognize clefts in targets. Together, this work illustrates the utilization of different surfaces of a single immunoglobulin-like scaffold to generate binding proteins with distinct characteristics.

-	~~==Disease==~~	+	Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.,Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S J Mol Biol. 2012 Jan 13;415(2):393-405. Epub 2011 Dec 16. PMID:22198408<ref>PMID:22198408</ref>
-	~~[[http~~:~~//www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause~~ of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[http://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the ~~upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum~~. ~~Note=~~A ~~chromosomal aberation involving SUMO1 is the cause of OFC10~~. ~~Translocation t~~(2;8)~~(q33~~.~~1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays~~.<ref>PMID:~~16990542~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~//www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, ~~and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in~~ a ~~number~~ of ~~cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to~~ the ~~nuclear pore complex protein RANBP2~~. ~~Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins~~. ~~May also regulate a network~~ of ~~genes involved in palate development~~.<~~ref~~>~~PMID:9019411~~</~~ref~~>~~<ref>PMID:9162015</ref><ref>PMID:18538659</ref><ref>PMID:18408734</ref>~~	+	</div>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	[[3rzw]] is a 4 chain structure with 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=3RZW OCA].	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	~~<ref group="xtra">PMID:022198408</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Gilbreth, R N.]]	+	[[Category: Gilbreth, R N]]
-	[[Category: Koide, S.]]	+	[[Category: Koide, S]]
	[[Category: Antibody mimic]]		[[Category: Antibody mimic]]
	[[Category: Beta grasp]]		[[Category: Beta grasp]]

OCA at 07:25, 25 March 2013

OCA — Mon, 25 Mar 2013 07:25:09 GMT

←Older revision		Revision as of 07:25, 25 March 2013
Line 1:		Line 1:
-	[[Image:3rzw.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3rzw", 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_3rzw\| PDB=3rzw \| SCENE= }}		{{STRUCTURE_3rzw\| PDB=3rzw \| SCENE= }}
-
	===Crystal Structure of the Monobody ySMB-9 bound to human SUMO1===		===Crystal Structure of the Monobody ySMB-9 bound to human SUMO1===
		+	{{ABSTRACT_PUBMED_22198408}}

		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:[http://omim.org/entry/613705 613705]]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.<ref>PMID:16990542</ref>

-	~~<!--~~	+	==Function==
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22198408}}, adds the Publication Abstract to the page~~	+	[[http://www.uniprot.org/uniprot/SUMO1_HUMAN SUMO1_HUMAN]] Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.<ref>PMID:9019411</ref><ref>PMID:9162015</ref><ref>PMID:18538659</ref><ref>PMID:18408734</ref>
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 22198408 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_22198408}}~~	+

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022198408</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022198408</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Gilbreth, R N.]]		[[Category: Gilbreth, R N.]]

OCA at 05:23, 23 May 2012

OCA — Wed, 23 May 2012 05:23:13 GMT

←Older revision		Revision as of 05:23, 23 May 2012
Line 1:		Line 1:
-	[[Image:3rzw.~~jpg~~\|left\|200px]]	+	[[Image:3rzw.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal Structure of the Monobody ySMB-9 bound to human SUMO1===		===Crystal Structure of the Monobody ySMB-9 bound to human SUMO1===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22198408}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22198408 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22198408}}

	==About this Structure==		==About this Structure==
	[[3rzw]] is a 4 chain structure with 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=3RZW OCA].		[[3rzw]] is a 4 chain structure with 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=3RZW OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022198408</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Gilbreth, R N.]]		[[Category: Gilbreth, R N.]]

OCA at 07:38, 28 December 2011

OCA — Wed, 28 Dec 2011 07:38:56 GMT

←Older revision		Revision as of 07:38, 28 December 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rzw.jpg\|left\|200px]]

-	The ~~entry 3rzw~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rzw", 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_3rzw\| PDB=3rzw \| SCENE= }}

-	~~Authors: Gilbreth, R.N., Koide, S.~~	+	===Crystal Structure of the Monobody ySMB-9 bound to human SUMO1===

-	~~Description: Crystal~~ Structure ~~of the Monobody ySMB~~-~~9 bound to human SUMO1~~	+
		+	==About this Structure==
		+	[[3rzw]] is a 4 chain structure with 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=3RZW OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Gilbreth, R N.]]
		+	[[Category: Koide, S.]]
		+	[[Category: Antibody mimic]]
		+	[[Category: Beta grasp]]
		+	[[Category: Beta sandwich]]
		+	[[Category: Engineered binding protein]]
		+	[[Category: Post-translational modification]]
		+	[[Category: Protein binding]]

OCA at 04:51, 8 June 2011

OCA — Wed, 08 Jun 2011 04:51:40 GMT

←Older revision		Revision as of 04:51, 8 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rzw is ON HOLD	+	The entry 3rzw is ON HOLD until Paper Publication

	Authors: Gilbreth, R.N., Koide, S.		Authors: Gilbreth, R.N., Koide, S.

	Description: Crystal Structure of the Monobody ySMB-9 bound to human SUMO1		Description: Crystal Structure of the Monobody ySMB-9 bound to human SUMO1

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

OCA — Wed, 18 May 2011 05:20:49 GMT

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

←Older revision

Revision as of 05:20, 18 May 2011