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Open data
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Basic information
Entry | Database: PDB / ID: 1miu | ||||||
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Title | Structure of a BRCA2-DSS1 complex | ||||||
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![]() | GENE REGULATION/ANTITUMOR PROTEIN / TUMOR SUPPRESSOR / BREAST CANCER SUSCEPTIBILITY / DNA-BINDING / GENE REGULATION-ANTITUMOR PROTEIN COMPLEX | ||||||
Function / homology | ![]() 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) / centrosome duplication / nuclear ubiquitin ligase complex / chordate embryonic development / lateral element / integrator complex / 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 / 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 / stem cell proliferation / secretory granule / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / cellular response to ionizing radiation / nucleotide-excision repair / Dectin-1 mediated noncanonical NF-kB signaling / response to gamma radiation / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / SCF(Skp2)-mediated degradation of p27/p21 / 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 / Orc1 removal from chromatin / 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 / brain development / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / multicellular organism growth Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.7 KB | Display | ![]() |
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PDB format | ![]() | 121.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8284.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 83350.562 Da / Num. of mol.: 1 / Fragment: Residues 2378-3115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-HG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.87 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Tris-HCl, CaCL2, NaCl, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 3.1→25 Å / Num. obs: 27074 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.046 |
Reflection shell | Resolution: 3.1→3.21 Å / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 25 Å / Redundancy: 5 % / Num. measured all: 136363 / Rmerge(I) obs: 0.046 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor all: 0.26 / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.256 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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