3q4f - Revision history

OCA at 10:45, 21 February 2024

2024-02-21T10:45:45Z

←Older revision		Revision as of 10:45, 21 February 2024
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	<StructureSection load='3q4f' size='340' side='right'caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>		<StructureSection load='3q4f' size='340' side='right'caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NHEJ1~~, ~~XLF (~~[~~https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=9606 HUMAN]), XRCC4 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=9606 HUMAN])~~</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]] 5.5Å</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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [https://pdbe.org/3q4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [https://www.ebi.ac.uk/pdbsum/3q4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4f 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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [https://pdbe.org/3q4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [https://www.ebi.ac.uk/pdbsum/3q4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4f ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] Defects in NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:[https://omim.org/entry/611291 611291]]; also known as autosomal recessive T-cell-negative, B-cell-negative, NK cell-positive, severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17317666</ref> <ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:12604777</ref>	+	[https://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN] Defects in NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:[https://omim.org/entry/611291 611291]; also known as autosomal recessive T-cell-negative, B-cell-negative, NK cell-positive, severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17317666</ref> <ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:12604777</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17470781</ref> [[https://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN]] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref> <ref>PMID:10854421</ref> <ref>PMID:10757784</ref> <ref>PMID:16412978</ref>	+	[https://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17470781</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X4(1-157)-Cernunnos(1-224) complex at 5.5-A resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X4(1-157) and Cernunnos(1-224) homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4-Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4-Cernunnos interface. We identified four X4 residues (Glu(55), Asp(58), Met(61), and Phe(106)) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step.	+
-		+
-	Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining.,Ropars V, Drevet P, Legrand P, Baconnais S, Amram J, Faure G, Marquez JA, Pietrement O, Guerois R, Callebaut I, Le Cam E, Revy P, de Villartay JP, Charbonnier JB Proc Natl Acad Sci U S A. 2011 Jul 18. PMID:21768349<ref>PMID:21768349</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3q4f" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Charbonnier~~, J B~~]]	+	[[Category: Charbonnier JB]]
-	[[Category: Legrand, P]]	+	[[Category: Legrand P]]
-	[[Category: Ropars, V]]	+	[[Category: Ropars V]]
-	~~[[Category: Dna binding protein-protein binding complex]]~~	+
-	~~[[Category: Dsb repair]]~~	+
-	~~[[Category: Nuclear]]~~	+
-	~~[[Category: Recombination-recombination complex~~]]	+

OCA at 05:51, 8 June 2022

2022-06-08T05:51:24Z

←Older revision		Revision as of 05:51, 8 June 2022
Line 1:		Line 1:

	==Crystal structure of xrcc4/xlf-cernunnos complex==		==Crystal structure of xrcc4/xlf-cernunnos complex==
-	<StructureSection load='3q4f' size='340' side='right' caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>	+	<StructureSection load='3q4f' size='340' side='right'caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NHEJ1, XLF ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), XRCC4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NHEJ1, XLF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), XRCC4 ([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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [~~http~~://pdbe.org/3q4f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3q4f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4f 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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [https://pdbe.org/3q4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [https://www.ebi.ac.uk/pdbsum/3q4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4f ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] Defects in NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:[~~http~~://omim.org/entry/611291 611291]]; also known as autosomal recessive T-cell-negative, B-cell-negative, NK cell-positive, severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17317666</ref> <ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:12604777</ref>	+	[[https://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] Defects in NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:[https://omim.org/entry/611291 611291]]; also known as autosomal recessive T-cell-negative, B-cell-negative, NK cell-positive, severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17317666</ref> <ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:12604777</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17470781</ref> [[~~http~~://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN]] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref> <ref>PMID:10854421</ref> <ref>PMID:10757784</ref> <ref>PMID:16412978</ref>	+	[[https://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17470781</ref> [[https://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN]] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref> <ref>PMID:10854421</ref> <ref>PMID:10757784</ref> <ref>PMID:16412978</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Charbonnier, J B]]		[[Category: Charbonnier, J B]]
	[[Category: Legrand, P]]		[[Category: Legrand, P]]

OCA at 00:00, 5 August 2016

2016-08-05T00:00:39Z

←Older revision		Revision as of 00:00, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of xrcc4/xlf-cernunnos complex==		==Crystal structure of xrcc4/xlf-cernunnos complex==
	<StructureSection load='3q4f' size='340' side='right' caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>		<StructureSection load='3q4f' size='340' side='right' caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NHEJ1, XLF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), XRCC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NHEJ1, XLF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), XRCC4 ([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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [http://www.ebi.ac.uk/pdbsum/3q4f 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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [http://pdbe.org/3q4f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [http://www.ebi.ac.uk/pdbsum/3q4f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4f ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 18:		Line 19:
	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 3q4f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Charbonnier, J B]]		[[Category: Charbonnier, J B]]
	[[Category: Legrand, P]]		[[Category: Legrand, P]]

OCA at 10:14, 19 December 2014

2014-12-19T10:14:27Z

←Older revision		Revision as of 10:14, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3q4f~~\| ~~PDB~~=3q4f \| ~~SCENE~~= }}	+	==Crystal structure of xrcc4/xlf-cernunnos complex==
-	===~~Crystal structure~~ of ~~xrcc4~~/~~xlf~~-~~cernunnos~~ complex===	+	<StructureSection load='3q4f' size='340' side='right' caption='[[3q4f]], [[Resolution\|resolution]] 5.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21768349}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3q4f]] is a 8 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=3Q4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q4F FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NHEJ1, XLF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), XRCC4 ([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=3q4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q4f RCSB], [http://www.ebi.ac.uk/pdbsum/3q4f PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] Defects in NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:[http://omim.org/entry/611291 611291]]; also known as autosomal recessive T-cell-negative, B-cell-negative, NK cell-positive, severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17317666</ref> <ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:12604777</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary.<ref>PMID:16439204</ref> <ref>PMID:16439205</ref> <ref>PMID:17470781</ref> [[http://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN]] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref> <ref>PMID:10854421</ref> <ref>PMID:10757784</ref> <ref>PMID:16412978</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X4(1-157)-Cernunnos(1-224) complex at 5.5-A resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X4(1-157) and Cernunnos(1-224) homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4-Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4-Cernunnos interface. We identified four X4 residues (Glu(55), Asp(58), Met(61), and Phe(106)) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step.

-	~~==Disease==~~	+	Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining.,Ropars V, Drevet P, Legrand P, Baconnais S, Amram J, Faure G, Marquez JA, Pietrement O, Guerois R, Callebaut I, Le Cam E, Revy P, de Villartay JP, Charbonnier JB Proc Natl Acad Sci U S A. 2011 Jul 18. PMID:21768349<ref>PMID:21768349</ref>
-	~~[[http:~~/~~/www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] Defects~~ in ~~NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1~~-~~SCID) [MIM:[http://omim~~.~~org/entry/611291 611291]]; also known as autosomal recessive T-cell-negative~~, ~~B-cell-negative~~, ~~NK cell-positive~~, ~~severe combined immunodeficiency with microcephaly~~, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, ~~leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent~~, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, ~~microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation~~, ~~probably due to hypomorphic NHEJ1 mutations~~.~~<ref>~~PMID:16439204</ref><ref>PMID:16439205</ref><ref>PMID:17317666</ref><ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:~~12604777~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~//www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a ~~bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration~~ of the ~~end bound NHEJ factors to allow XRCC4 access to the DNA termini~~. ~~It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary~~.<ref>PMID:16439204</ref><ref>PMID:16439205</ref><ref>PMID:17470781</ref> [[http://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN]] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of ~~LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends~~.<~~ref~~>~~PMID:8548796~~</~~ref~~>~~<ref>PMID:10854421</ref><ref>PMID:10757784</ref><ref>PMID:16412978</ref>~~	+	</div>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	[[3q4f]] is a 8 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=3Q4F OCA].	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	~~<ref group="xtra">PMID:021768349</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Charbonnier, J B.]]	+	[[Category: Charbonnier, J B]]
-	[[Category: Legrand, P.]]	+	[[Category: Legrand, P]]
-	[[Category: Ropars, V.]]	+	[[Category: Ropars, V]]
	[[Category: Dna binding protein-protein binding complex]]		[[Category: Dna binding protein-protein binding complex]]
	[[Category: Dsb repair]]		[[Category: Dsb repair]]
	[[Category: Nuclear]]		[[Category: Nuclear]]
	[[Category: Recombination-recombination complex]]		[[Category: Recombination-recombination complex]]

OCA at 05:25, 25 March 2013

2013-03-25T05:25:54Z

←Older revision		Revision as of 05:25, 25 March 2013
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-	[[Image:3q4f.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3q4f", 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_3q4f\| PDB=3q4f \| SCENE= }}		{{STRUCTURE_3q4f\| PDB=3q4f \| SCENE= }}
-
	===Crystal structure of xrcc4/xlf-cernunnos complex===		===Crystal structure of xrcc4/xlf-cernunnos complex===
		+	{{ABSTRACT_PUBMED_21768349}}

		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] Defects in NHEJ1 are the cause of severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:[http://omim.org/entry/611291 611291]]; also known as autosomal recessive T-cell-negative, B-cell-negative, NK cell-positive, severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation or NHEJ1 syndrome. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.<ref>PMID:16439204</ref><ref>PMID:16439205</ref><ref>PMID:17317666</ref><ref>PMID:12604777</ref> Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).<ref>PMID:12604777</ref>

-	~~<!--~~	+	==Function==
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21768349}}~~, ~~adds~~ the ~~Publication Abstract~~ to the ~~page~~	+	[[http://www.uniprot.org/uniprot/NHEJ1_HUMAN NHEJ1_HUMAN]] DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary.<ref>PMID:16439204</ref><ref>PMID:16439205</ref><ref>PMID:17470781</ref> [[http://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN]] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref><ref>PMID:10854421</ref><ref>PMID:10757784</ref><ref>PMID:16412978</ref>
-	(~~as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 21768349~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21768349}}~~	+

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021768349</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021768349</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Charbonnier, J B.]]		[[Category: Charbonnier, J B.]]

OCA at 07:33, 2 November 2011

2011-11-02T07:33:27Z

←Older revision		Revision as of 07:33, 2 November 2011
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-	[[Image:3q4f.~~jpg~~\|left\|200px]]	+	[[Image:3q4f.png\|left\|200px]]

	<!--		<!--

OCA at 08:47, 3 August 2011

2011-08-03T08:47:06Z

←Older revision		Revision as of 08:47, 3 August 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3q4f.jpg\|left\|200px]]

-	The ~~entry 3q4f~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3q4f", 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_3q4f\| PDB=3q4f \| SCENE= }}

-	~~Authors: Ropars, V., Legrand, P., Charbonnier, J.B.~~	+	===Crystal structure of xrcc4/xlf-cernunnos complex===

-	~~Description~~: ~~Crystal~~ structure ~~of xrcc4~~/~~xlf~~-~~cernunnos~~ complex	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21768349}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21768349 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21768349}}
		+
		+	==About this Structure==
		+	[[3q4f]] is a 8 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=3Q4F OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021768349</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Charbonnier, J B.]]
		+	[[Category: Legrand, P.]]
		+	[[Category: Ropars, V.]]
		+	[[Category: Dna binding protein-protein binding complex]]
		+	[[Category: Dsb repair]]
		+	[[Category: Nuclear]]
		+	[[Category: Recombination-recombination complex]]

OCA at 05:33, 27 July 2011

2011-07-27T05:33:23Z

←Older revision		Revision as of 05:33, 27 July 2011
Line 3:		Line 3:
	The entry 3q4f is ON HOLD until Paper Publication		The entry 3q4f is ON HOLD until Paper Publication

-	Authors: Ropars, V~~., Drevet, P~~., Legrand, ~~P., Baconnais, S., Faure, G., Marquez, J.A., Pi trement, O., Guerois, R., Callebaut, I., Le Cam, E., Revy, P., de Villartay, J.~~P., Charbonnier, J.B.	+	Authors: Ropars, V., Legrand, P., Charbonnier, J.B.

-	Description: Crystal structure of ~~a DNA repair~~ complex	+	Description: Crystal structure of xrcc4/xlf-cernunnos complex

OCA at 08:01, 16 March 2011

2011-03-16T08:01:05Z

←Older revision		Revision as of 08:01, 16 March 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3q4f is ON HOLD	+	The entry 3q4f is ON HOLD until Paper Publication

	Authors: Ropars, V., Drevet, P., Legrand, P., Baconnais, S., Faure, G., Marquez, J.A., Pi trement, O., Guerois, R., Callebaut, I., Le Cam, E., Revy, P., de Villartay, J.P., Charbonnier, J.B.		Authors: Ropars, V., Drevet, P., Legrand, P., Baconnais, S., Faure, G., Marquez, J.A., Pi trement, O., Guerois, R., Callebaut, I., Le Cam, E., Revy, P., de Villartay, J.P., Charbonnier, J.B.

	Description: Crystal structure of a DNA repair complex		Description: Crystal structure of a DNA repair complex

OCA: Protected "3q4f" [edit=sysop:move=sysop]

2010-12-29T18:18:51Z

Protected "3q4f" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:18, 29 December 2010