2qm4

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[[Image:2qm4.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor==
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|PDB= 2qm4 |SIZE=350|CAPTION= <scene name='initialview01'>2qm4</scene>, resolution 2.30&Aring;
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<StructureSection load='2qm4' size='340' side='right'caption='[[2qm4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[2qm4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QM4 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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|GENE= NHEJ1, XLF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qm4 OCA], [https://pdbe.org/2qm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qm4 RCSB], [https://www.ebi.ac.uk/pdbsum/2qm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qm4 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1fu1|1fu1]], [[1ik9|1ik9]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qm4 OCA], [http://www.ebi.ac.uk/pdbsum/2qm4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qm4 RCSB]</span>
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== Disease ==
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}}
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[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>
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== Function ==
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'''Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor'''
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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==Overview==
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qm/2qm4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2qm4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
The recently characterised 299-residue human XLF/Cernunnos protein plays a crucial role in DNA repair by non-homologous end joining (NHEJ) and interacts with the XRCC4-DNA Ligase IV complex. Here, we report the crystal structure of the XLF (1-233) homodimer at 2.3 A resolution, confirming the predicted structural similarity to XRCC4. The XLF coiled-coil, however, is shorter than that of XRCC4 and undergoes an unexpected reverse in direction giving rise to a short distorted four helical bundle and a C-terminal helical structure wedged between the coiled-coil and head domain. The existence of a dimer as the major species is confirmed by size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering and other biophysical methods. We show that the XLF structure is not easily compatible with a proposed XRCC4:XLF heterodimer. However, we demonstrate interactions between dimers of XLF and XRCC4 by surface plasmon resonance and analyse these in terms of surface properties, amino-acid conservation and mutations in immunodeficient patients. Our data are most consistent with head-to-head interactions in a 2:2:1 XRCC4:XLF:Ligase IV complex.
The recently characterised 299-residue human XLF/Cernunnos protein plays a crucial role in DNA repair by non-homologous end joining (NHEJ) and interacts with the XRCC4-DNA Ligase IV complex. Here, we report the crystal structure of the XLF (1-233) homodimer at 2.3 A resolution, confirming the predicted structural similarity to XRCC4. The XLF coiled-coil, however, is shorter than that of XRCC4 and undergoes an unexpected reverse in direction giving rise to a short distorted four helical bundle and a C-terminal helical structure wedged between the coiled-coil and head domain. The existence of a dimer as the major species is confirmed by size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering and other biophysical methods. We show that the XLF structure is not easily compatible with a proposed XRCC4:XLF heterodimer. However, we demonstrate interactions between dimers of XLF and XRCC4 by surface plasmon resonance and analyse these in terms of surface properties, amino-acid conservation and mutations in immunodeficient patients. Our data are most consistent with head-to-head interactions in a 2:2:1 XRCC4:XLF:Ligase IV complex.
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==About this Structure==
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Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ.,Li Y, Chirgadze DY, Bolanos-Garcia VM, Sibanda BL, Davies OR, Ahnesorg P, Jackson SP, Blundell TL EMBO J. 2008 Jan 9;27(1):290-300. Epub 2007 Nov 29. PMID:18046455<ref>PMID:18046455</ref>
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2QM4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QM4 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ., Li Y, Chirgadze DY, Bolanos-Garcia VM, Sibanda BL, Davies OR, Ahnesorg P, Jackson SP, Blundell TL, EMBO J. 2008 Jan 9;27(1):290-300. Epub 2007 Nov 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18046455 18046455]
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</div>
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<div class="pdbe-citations 2qm4" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Blundell, T L.]]
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[[Category: Blundell TL]]
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[[Category: Bolanos-Garcia, V M.]]
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[[Category: Bolanos-Garcia VM]]
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[[Category: Chirgadze, D Y.]]
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[[Category: Chirgadze DY]]
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[[Category: Davies, O R.]]
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[[Category: Davies OR]]
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[[Category: Li, Y.]]
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[[Category: Li Y]]
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[[Category: Sibanda, B L.]]
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[[Category: Sibanda BL]]
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[[Category: beta-sandwich]]
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[[Category: coiled-coil]]
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[[Category: homodimer]]
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[[Category: recombination]]
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[[Category: xrcc4 like factor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:50:47 2008''
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Current revision

Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor

PDB ID 2qm4

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