+Open data
-Basic information
Entry | Database: PDB / ID: 1mje | ||||||
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Title | STRUCTURE OF A BRCA2-DSS1-SSDNA COMPLEX | ||||||
Components |
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Keywords | GENE REGULATION/ANTITUMOR PROTEIN/DNA / TUMOR SUPPRESSOR / BREAST CANCER SUSCEPTIBILITY / DNA-BINDING / GENE REGULATION-ANTITUMOR PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information HDR through MMEJ (alt-NHEJ) / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / homologous chromosome orientation in meiotic metaphase I / BRCA2-MAGE-D1 complex / HDR through Homologous Recombination (HRR) / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere ...HDR through MMEJ (alt-NHEJ) / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / homologous chromosome orientation in meiotic metaphase I / BRCA2-MAGE-D1 complex / HDR through Homologous Recombination (HRR) / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear ubiquitin ligase complex / chordate embryonic development / integrator complex / lateral element / telomere maintenance via recombination / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / mammary gland development / proteasome regulatory particle, lid subcomplex / gamma-tubulin binding / DNA repair complex / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / oocyte maturation / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / inner cell mass cell proliferation / Somitogenesis / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / female gonad development / replication fork processing / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / hemopoiesis / response to X-ray / proteasome assembly / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mRNA export from nucleus / positive regulation of mitotic cell cycle / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / regulation of cytokinesis / Autodegradation of Cdh1 by Cdh1:APC/C / stem cell proliferation / APC/C:Cdc20 mediated degradation of Securin / secretory granule / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / cellular response to ionizing radiation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / nucleotide-excision repair / Hh mutants are degraded by ERAD / response to gamma radiation / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / double-strand break repair via homologous recombination / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / HDR through Homologous Recombination (HRR) / multicellular organism growth / brain development / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Yang, H. / Jeffrey, P.D. / Miller, J. / Kinnucan, E. / Sun, Y. / Thoma, N.H. / Zheng, N. / Chen, P.L. / Lee, W.H. / Pavletich, N.P. | ||||||
Citation | Journal: Science / Year: 2002 Title: BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Authors: Yang, H. / Jeffrey, P.D. / Miller, J. / Kinnucan, E. / Sun, Y. / Thoma, N.H. / Zheng, N. / Chen, P.L. / Lee, W.H. / Pavletich, N.P. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUES 2793-2879 OF THE BRCA2 CHAIN WERE REMOVED PROTEOLYTICALLY. RESIDUES 3087 AND 3089 ...SEQUENCE RESIDUES 2793-2879 OF THE BRCA2 CHAIN WERE REMOVED PROTEOLYTICALLY. RESIDUES 3087 AND 3089 ARE COVALENTLY BOUND. 3088 WAS SKIPPED IN THE NUMBERING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mje.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mje.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mje_validation.pdf.gz | 386.7 KB | Display | wwPDB validaton report |
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Full document | 1mje_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 1mje_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1mje_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mje ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mje | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 8284.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60896 |
#3: Protein | Mass: 72983.172 Da / Num. of mol.: 1 Fragment: sequence database residues 2378-2792, 2880-3113 (residues 2793-2879 removed) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 17973451, UniProt: P97929*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.95 Å3/Da / Density % sol: 79.34 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Sodium Acetate, Sodium Citrate, NaCl, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→25 Å / Num. all: 24950 / Num. obs: 24950 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.5→3.62 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.5→15 Å
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Refine LS restraints |
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