5ybc - Revision history

OCA at 10:22, 27 March 2024

2024-03-27T10:22:38Z

←Older revision		Revision as of 10:22, 27 March 2024
Line 1:		Line 1:

	==X-ray structure of native ETS-domain domain of Ergp55==		==X-ray structure of native ETS-domain domain of Ergp55==
-	<StructureSection load='5ybc' size='340' side='right' caption='[[5ybc]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5ybc' size='340' side='right'caption='[[5ybc]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ybc]] is a 2 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=5YBC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ybc]] is a 2 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=5YBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YBC 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ERG ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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='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=5ybc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybc OCA], [~~http~~://pdbe.org/5ybc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ybc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ybc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybc 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=5ybc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybc OCA], [https://pdbe.org/5ybc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ybc RCSB], [https://www.ebi.ac.uk/pdbsum/5ybc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybc ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN]] Defects in ERG are a cause of Ewing sarcoma (ES) [MIM:[~~http~~://omim.org/entry/612219 612219]]. A highly malignant, metastatic, primitive small round cell tumor of bone and soft tissue that affects children and adolescents. It belongs to the Ewing sarcoma family of tumors, a group of morphologically heterogeneous neoplasms that share the same cytogenetic features. They are considered neural tumors derived from cells of the neural crest. Ewing sarcoma represents the less differentiated form of the tumors. Note=A chromosomal aberration involving ERG is found in patients with Erwing sarcoma. Translocation t(21;22)(q22;q12) with EWSR1. Note=Chromosomal aberrations involving ERG have been found in acute myeloid leukemia (AML). Translocation t(16;21)(p11;q22) with FUS. Translocation t(X;21)(q25-26;q22) with ELF4.	+	[https://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN] Defects in ERG are a cause of Ewing sarcoma (ES) [MIM:[https://omim.org/entry/612219 612219]. A highly malignant, metastatic, primitive small round cell tumor of bone and soft tissue that affects children and adolescents. It belongs to the Ewing sarcoma family of tumors, a group of morphologically heterogeneous neoplasms that share the same cytogenetic features. They are considered neural tumors derived from cells of the neural crest. Ewing sarcoma represents the less differentiated form of the tumors. Note=A chromosomal aberration involving ERG is found in patients with Erwing sarcoma. Translocation t(21;22)(q22;q12) with EWSR1. Note=Chromosomal aberrations involving ERG have been found in acute myeloid leukemia (AML). Translocation t(16;21)(p11;q22) with FUS. Translocation t(X;21)(q25-26;q22) with ELF4.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN]] Transcriptional regulator. May participate in transcriptional regulation through the recruitment of SETDB1 histone methyltransferase and subsequent modification of local chromatin structure.	+	[https://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN] Transcriptional regulator. May participate in transcriptional regulation through the recruitment of SETDB1 histone methyltransferase and subsequent modification of local chromatin structure.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P41212 and of its complex with the E74 DNA sequence (DNA9) in space group C2221 were obtained and their structures were determined. Comparative structure analysis of the ETSi domain and its complex with DNA9 with previously determined structures of the ERGi domain (the ETS domain of ERG containing inhibitory motifs) in space group P65212 and of the ERGi-DNA12 complex in space group P41212 were performed. The ETSi domain is observed as a homodimer in solution as well as in the crystallographic asymmetric unit. Superposition of the structure of the ETSi domain on that of the ERGi domain showed a major conformational change at the C-terminal DNA-binding autoinhibitory (CID) motif, while minor changes are observed in the loop regions of the ETSi-domain structure. The ETSi-DNA9 complex in space group C2221 forms a structure that is quite similar to that of the ERG-DNA12 complex in space group P41212. Upon superposition of the complexes, major conformational changes are observed at the 5' and 3' ends of DNA9, while the conformation of the core GGA nucleotides was quite conserved. Comparison of the ETSi-DNA9 structure with known structures of ETS class 1 protein-DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.	+
-		+
-	Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence.,Sharma R, Gangwar SP, Saxena AK Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):656-663. doi:, 10.1107/S2053230X1801110X. Epub 2018 Sep 21. PMID:30279318<ref>PMID:30279318</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5ybc" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Gangwar, S P~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Saxena, A K~~]]	+	[[Category: Gangwar SP]]
-	[[Category: ~~Ergp55]]~~	+	[[Category: Saxena AK]]
-	~~[[Category: Ets transcription factor]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 08:29, 17 October 2018

2018-10-17T08:29:53Z

←Older revision		Revision as of 08:29, 17 October 2018
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	<StructureSection load='5ybc' size='340' side='right' caption='[[5ybc]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5ybc' size='340' side='right' caption='[[5ybc]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ybc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ybc]] is a 2 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=5YBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBC 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERG ([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=5ybc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybc OCA], [http://pdbe.org/5ybc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybc RCSB], [http://www.ebi.ac.uk/pdbsum/5ybc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybc 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=5ybc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybc OCA], [http://pdbe.org/5ybc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybc RCSB], [http://www.ebi.ac.uk/pdbsum/5ybc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybc ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN]] Transcriptional regulator. May participate in transcriptional regulation through the recruitment of SETDB1 histone methyltransferase and subsequent modification of local chromatin structure.		[[http://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN]] Transcriptional regulator. May participate in transcriptional regulation through the recruitment of SETDB1 histone methyltransferase and subsequent modification of local chromatin structure.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P41212 and of its complex with the E74 DNA sequence (DNA9) in space group C2221 were obtained and their structures were determined. Comparative structure analysis of the ETSi domain and its complex with DNA9 with previously determined structures of the ERGi domain (the ETS domain of ERG containing inhibitory motifs) in space group P65212 and of the ERGi-DNA12 complex in space group P41212 were performed. The ETSi domain is observed as a homodimer in solution as well as in the crystallographic asymmetric unit. Superposition of the structure of the ETSi domain on that of the ERGi domain showed a major conformational change at the C-terminal DNA-binding autoinhibitory (CID) motif, while minor changes are observed in the loop regions of the ETSi-domain structure. The ETSi-DNA9 complex in space group C2221 forms a structure that is quite similar to that of the ERG-DNA12 complex in space group P41212. Upon superposition of the complexes, major conformational changes are observed at the 5' and 3' ends of DNA9, while the conformation of the core GGA nucleotides was quite conserved. Comparison of the ETSi-DNA9 structure with known structures of ETS class 1 protein-DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.
		+
		+	Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence.,Sharma R, Gangwar SP, Saxena AK Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):656-663. doi:, 10.1107/S2053230X1801110X. Epub 2018 Sep 21. PMID:30279318<ref>PMID:30279318</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ybc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Gangwar, S P]]		[[Category: Gangwar, S P]]
	[[Category: Saxena, A K]]		[[Category: Saxena, A K]]

OCA at 19:37, 19 September 2018

2018-09-19T19:37:36Z

←Older revision		Revision as of 19:37, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ybc is ~~ON HOLD~~ ~~until Paper Publication~~	+	==X-ray structure of native ETS-domain domain of Ergp55==
-		+	<StructureSection load='5ybc' size='340' side='right' caption='[[5ybc]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ybc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBC FirstGlance]. <br>
-	~~Description~~:	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5ybc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybc OCA], [http://pdbe.org/5ybc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybc RCSB], [http://www.ebi.ac.uk/pdbsum/5ybc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybc ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN]] Defects in ERG are a cause of Ewing sarcoma (ES) [MIM:[http://omim.org/entry/612219 612219]]. A highly malignant, metastatic, primitive small round cell tumor of bone and soft tissue that affects children and adolescents. It belongs to the Ewing sarcoma family of tumors, a group of morphologically heterogeneous neoplasms that share the same cytogenetic features. They are considered neural tumors derived from cells of the neural crest. Ewing sarcoma represents the less differentiated form of the tumors. Note=A chromosomal aberration involving ERG is found in patients with Erwing sarcoma. Translocation t(21;22)(q22;q12) with EWSR1. Note=Chromosomal aberrations involving ERG have been found in acute myeloid leukemia (AML). Translocation t(16;21)(p11;q22) with FUS. Translocation t(X;21)(q25-26;q22) with ELF4.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ERG_HUMAN ERG_HUMAN]] Transcriptional regulator. May participate in transcriptional regulation through the recruitment of SETDB1 histone methyltransferase and subsequent modification of local chromatin structure.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gangwar, S P]]
		+	[[Category: Saxena, A K]]
		+	[[Category: Ergp55]]
		+	[[Category: Ets transcription factor]]
		+	[[Category: Structural protein]]

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

2017-09-27T16:22:11Z

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

←Older revision

Revision as of 16:22, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ybc is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T16:22:10Z

New page: '''Unreleased structure''' The entry 5ybc is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ybc is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]