3cmy - Revision history

OCA at 09:36, 21 February 2024

2024-02-21T09:36:49Z

←Older revision		Revision as of 09:36, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3cmy' size='340' side='right'caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3cmy' size='340' side='right'caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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]] 1.95Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PAX3 ([https~~:/~~/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=EDO:1,2-ETHANEDIOL'>EDO</scene></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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [https://pdbe.org/3cmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [https://www.ebi.ac.uk/pdbsum/3cmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmy 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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [https://pdbe.org/3cmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [https://www.ebi.ac.uk/pdbsum/3cmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[https://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[https://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[https://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[https://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.	+	[https://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[https://omim.org/entry/193500 193500]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[https://omim.org/entry/148820 148820]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[https://omim.org/entry/122880 122880]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[https://omim.org/entry/268220 268220]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.	+	[https://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 22:
	</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=3cmy 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=3cmy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The transcription regulatory protein PAX3 binds to cognate DNA sequences through two DNA-binding domains, a paired domain and a homeodomain, and has important functions during neurogenesis and myogenesis. In humans, mutations in the PAX3 gene cause Waardenburg syndrome, whereas a chromosomal translocation that generates a PAX3-FOXO1 fusion gene is associated with the development of alveolar rhabdomyosarcoma. We have determined the crystal structure of the human PAX3 homeodomain in complex with a palindromic DNA containing two inverted TAATC sequences at 1.95 A resolution. Two homeodomains bind to DNA as a symmetric dimer, inducing a 3 degrees bend in the DNA helix. The N-terminal arm of the homeodomain inserts into the minor groove and makes direct and water-mediated interactions with bases and the sugar-phosphate backbone. The recognition helix fits directly into the major groove, and an elaborate network of structurally conserved water molecules mediates the majority of protein-DNA interactions. The structure elucidates the role of serine 50 in selection of the CG sequence immediately 3' of the TAAT motif by PAX class homeodomains and provides insights into the molecular mechanisms by which certain Waardenburg syndrome-associated missense mutations could destabilize the fold of the PAX3 homeodomain whereas others could affect its interaction with DNA.
-
-	Structural Basis for DNA Recognition by the Human PAX3 Homeodomain (dagger) (,) (double dagger).,Birrane G, Soni A, Ladias JA Biochemistry. 2009 Jan 21. PMID:19199574<ref>PMID:19199574</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3cmy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Birrane, G]]	+	[[Category: Birrane G]]
-	[[Category: Ladias~~, J A.A~~]]	+	[[Category: Ladias JAA]]
-	[[Category: Soni, A]]	+	[[Category: Soni A]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna-binding protein]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription regulator-dna complex~~]]	+

OCA at 08:01, 27 January 2022

2022-01-27T08:01:45Z

←Older revision		Revision as of 08:01, 27 January 2022
Line 1:		Line 1:

	==Structure of a homeodomain in complex with DNA==		==Structure of a homeodomain in complex with DNA==
-	<StructureSection load='3cmy' size='340' side='right' caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3cmy' size='340' side='right'caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CMY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAX3 ([~~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">PAX3 ([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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [~~http~~://pdbe.org/3cmy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3cmy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmy 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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [https://pdbe.org/3cmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [https://www.ebi.ac.uk/pdbsum/3cmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[~~http~~://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[~~http~~://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[~~http~~://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[~~http~~://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.	+	[[https://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[https://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[https://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[https://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[https://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.	+	[[https://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Birrane, G]]		[[Category: Birrane, G]]
	[[Category: Ladias, J A.A]]		[[Category: Ladias, J A.A]]

OCA at 13:48, 7 November 2018

2018-11-07T13:48:29Z

←Older revision		Revision as of 13:48, 7 November 2018
Line 1:		Line 1:
		+
	==Structure of a homeodomain in complex with DNA==		==Structure of a homeodomain in complex with DNA==
	<StructureSection load='3cmy' size='340' side='right' caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3cmy' size='340' side='right' caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAX3 ([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">PAX3 ([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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://pdbe.org/3cmy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy 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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://pdbe.org/3cmy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/3cmy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/3cmy_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 01:48, 10 February 2016

2016-02-10T01:48:40Z

←Older revision		Revision as of 01:48, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3cmy' size='340' side='right' caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3cmy' size='340' side='right' caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAX3 ([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">PAX3 ([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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy 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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://pdbe.org/3cmy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 19:		Line 19:
	<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=3cmy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3cmy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Birrane, G]]		[[Category: Birrane, G]]
	[[Category: Ladias, J A.A]]		[[Category: Ladias, J A.A]]

OCA at 11:35, 20 January 2015

2015-01-20T11:35:52Z

←Older revision		Revision as of 11:35, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAX3 ([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">PAX3 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy 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=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[http://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[http://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[http://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[http://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.		[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[http://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[http://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[http://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[http://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Birrane, G.]]	+	[[Category: Birrane, G]]
-	[[Category: Ladias, J A.A.]]	+	[[Category: Ladias, J A.A]]
-	[[Category: Soni, A.]]	+	[[Category: Soni, A]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transcription regulator-dna complex]]		[[Category: Transcription regulator-dna complex]]

OCA at 21:22, 2 October 2014

2014-10-02T21:22:25Z

←Older revision		Revision as of 21:22, 2 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3cmy~~\| ~~PDB~~=3cmy \| ~~SCENE~~= }}	+	==Structure of a homeodomain in complex with DNA==
-	===~~Structure~~ of a homeodomain in complex with DNA~~===~~	+	<StructureSection load='3cmy' size='340' side='right' caption='[[3cmy]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19199574}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3cmy]] is a 3 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=3CMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAX3 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmy RCSB], [http://www.ebi.ac.uk/pdbsum/3cmy PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[http://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref> <ref>PMID:1347148</ref> <ref>PMID:1303193</ref> <ref>PMID:1347149</ref> <ref>PMID:8490648</ref> <ref>PMID:8447316</ref> <ref>PMID:7833953</ref> <ref>PMID:7825605</ref> <ref>PMID:8533800</ref> <ref>PMID:8589691</ref> <ref>PMID:8845842</ref> <ref>PMID:9067759</ref> <ref>PMID:9452070</ref> <ref>PMID:9541113</ref> [:]<ref>PMID:10779847</ref> <ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[http://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[http://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[http://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.
		+	== 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/cm/3cmy_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 ==
		+	The transcription regulatory protein PAX3 binds to cognate DNA sequences through two DNA-binding domains, a paired domain and a homeodomain, and has important functions during neurogenesis and myogenesis. In humans, mutations in the PAX3 gene cause Waardenburg syndrome, whereas a chromosomal translocation that generates a PAX3-FOXO1 fusion gene is associated with the development of alveolar rhabdomyosarcoma. We have determined the crystal structure of the human PAX3 homeodomain in complex with a palindromic DNA containing two inverted TAATC sequences at 1.95 A resolution. Two homeodomains bind to DNA as a symmetric dimer, inducing a 3 degrees bend in the DNA helix. The N-terminal arm of the homeodomain inserts into the minor groove and makes direct and water-mediated interactions with bases and the sugar-phosphate backbone. The recognition helix fits directly into the major groove, and an elaborate network of structurally conserved water molecules mediates the majority of protein-DNA interactions. The structure elucidates the role of serine 50 in selection of the CG sequence immediately 3' of the TAAT motif by PAX class homeodomains and provides insights into the molecular mechanisms by which certain Waardenburg syndrome-associated missense mutations could destabilize the fold of the PAX3 homeodomain whereas others could affect its interaction with DNA.

-	~~==Disease==~~	+	Structural Basis for DNA Recognition by the Human PAX3 Homeodomain (dagger) (,) (double dagger).,Birrane G, Soni A, Ladias JA Biochemistry. 2009 Jan 21. PMID:19199574<ref>PMID:19199574</ref>
-	~~[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in~~ PAX3 ~~are the cause of Waardenburg syndrome type 1~~ (~~WS1~~) ~~[MIM:[http://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye~~ (~~dystopia canthorum)~~, pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref><ref>PMID:1347148</ref><ref>PMID:1303193</ref><ref>PMID:1347149</ref><ref>PMID:8490648</ref><ref>PMID:8447316</ref><ref>PMID:7833953</ref><ref>PMID:7825605</ref><ref>PMID:8533800</ref><ref>PMID:8589691</ref><ref>PMID:8845842</ref><ref>PMID:9067759</ref><ref>PMID:9452070</ref><ref>PMID:9541113</ref>[:]<ref>PMID:10779847</ref><ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[http://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (~~CDHS~~) ~~[MIM:[http://omim~~.~~org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones~~, ~~hypoplastic maxilla~~, ~~small and short nose with thin nares~~, ~~limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness~~.<ref>PMID:~~8664898~~</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[http://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.	+
-		+
-	~~==Function==~~	+
-	~~[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3cmy]] is~~ a ~~3 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=3CMY OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:019199574</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Paired box protein\|Paired box protein]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Birrane, G.]]		[[Category: Birrane, G.]]

OCA at 22:15, 24 March 2013

2013-03-24T22:15:16Z

←Older revision		Revision as of 22:15, 24 March 2013
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-	[[Image:3cmy.png\|left\|200px]]
-
	{{STRUCTURE_3cmy\| PDB=3cmy \| SCENE= }}		{{STRUCTURE_3cmy\| PDB=3cmy \| SCENE= }}
-
	===Structure of a homeodomain in complex with DNA===		===Structure of a homeodomain in complex with DNA===
		+	{{ABSTRACT_PUBMED_19199574}}

-	~~{{ABSTRACT_PUBMED_19199574}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Defects in PAX3 are the cause of Waardenburg syndrome type 1 (WS1) [MIM:[http://omim.org/entry/193500 193500]]. WS1 is an autosomal dominant disorder characterized by wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum), pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma and sensorineural deafness. The syndrome shows variable clinical expression and some affected individuals do not manifest hearing impairment.<ref>PMID:7981674</ref><ref>PMID:1347148</ref><ref>PMID:1303193</ref><ref>PMID:1347149</ref><ref>PMID:8490648</ref><ref>PMID:8447316</ref><ref>PMID:7833953</ref><ref>PMID:7825605</ref><ref>PMID:8533800</ref><ref>PMID:8589691</ref><ref>PMID:8845842</ref><ref>PMID:9067759</ref><ref>PMID:9452070</ref><ref>PMID:9541113</ref>[:]<ref>PMID:10779847</ref><ref>PMID:12949970</ref> Defects in PAX3 are the cause of Waardenburg syndrome type 3 (WS3) [MIM:[http://omim.org/entry/148820 148820]]; also known as Klein-Waardenburg syndrome or Waardenburg syndrome with upper limb anomalies or white forelock with malformations. WS3 is a very rare autosomal dominant disorder, which shares many of the characteristics of WS1. Patients additionally present with musculoskeletal abnormalities. Defects in PAX3 are the cause of craniofacial-deafness-hand syndrome (CDHS) [MIM:[http://omim.org/entry/122880 122880]]. CDHS is thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness.<ref>PMID:8664898</ref> Defects in PAX3 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:[http://omim.org/entry/268220 268220]]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/PAX3_HUMAN PAX3_HUMAN]] Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

	==About this Structure==		==About this Structure==
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	==Reference==		==Reference==
-	<ref group="xtra">PMID:019199574</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019199574</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Birrane, G.]]		[[Category: Birrane, G.]]

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

2013-01-07T23:05:57Z

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

←Older revision

Revision as of 23:05, 7 January 2013

OCA at 23:05, 7 January 2013

2013-01-07T23:05:53Z

←Older revision		Revision as of 23:05, 7 January 2013
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-	{{Seed}}
	[[Image:3cmy.png\|left\|200px]]		[[Image:3cmy.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3cmy", creates the "Structure Box" on the page.
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_3cmy\| PDB=3cmy \| SCENE= }}		{{STRUCTURE_3cmy\| PDB=3cmy \| SCENE= }}

	===Structure of a homeodomain in complex with DNA===		===Structure of a homeodomain in complex with DNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19199574}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19199574 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19199574}}		{{ABSTRACT_PUBMED_19199574}}
-
-	==Disease==
-	Known disease associated with this structure: Craniofacial-deafness-hand syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=606597 606597]], Rhabdomyosarcoma, alveolar OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=606597 606597]], Waardenburg syndrome, type I OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=606597 606597]], Waardenburg syndrome, type III OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=606597 606597]]

	==About this Structure==		==About this Structure==
-	~~3CMY~~ is a 3 ~~chains~~ structure ~~of sequences~~ 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=3CMY OCA].	+	[[3cmy]] is a 3 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=3CMY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19199574~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019199574</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Birrane, G.]]		[[Category: Birrane, G.]]
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	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
-	[[Category: Paired box]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Transcription regulator/dna complex]]	+	[[Category: Transcription regulator-dna complex]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 3 08:58:49 2009''~~	+

OCA at 05:58, 3 June 2009

2009-06-03T05:58:49Z

←Older revision		Revision as of 05:58, 3 June 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3cmy.~~jpg~~\|left\|200px]]	+	[[Image:3cmy.png\|left\|200px]]

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	[[Category: Transcription regulator/dna complex]]		[[Category: Transcription regulator/dna complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 18 09~~:04:45 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 3 08:58:49 2009''