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Open data
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Basic information
Entry | Database: PDB / ID: 7ldg | ||||||||||||
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Title | Crystal structure of the MEILB2-BRCA2 complex | ||||||||||||
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![]() | RECOMBINATION / Complex / Recruiter / Protein-protein interaction / Armadillo-repeat | ||||||||||||
Function / homology | ![]() BRCA2-MAGE-D1 complex / 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) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination ...BRCA2-MAGE-D1 complex / 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) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA repair complex / female meiosis I / 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 / 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 / inner cell mass cell proliferation / 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 / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / brain development / Meiotic recombination / cellular senescence / double-strand break repair / chromosome / single-stranded DNA binding / spermatogenesis / protease binding / transcription by RNA polymerase II / chromosome, telomeric region / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Nandakumar, J. / Pendlebury, D.F. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites. Authors: Pendlebury, D.F. / Zhang, J. / Agrawal, R. / Shibuya, H. / Nandakumar, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.8 KB | Display | ![]() |
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PDB format | ![]() | 84.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.8 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28304.908 Da / Num. of mol.: 2 / Fragment: aa83-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 7738.730 Da / Num. of mol.: 2 / Fragment: MEILB2-binding domain (aa2271-2335) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate (pH 4.6), 2 M lithium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→89.94 Å / Num. obs: 35987 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.56→2.7 Å / Redundancy: 21.7 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 2 / Num. unique obs: 5188 / CC1/2: 0.833 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 96.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→31.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.63 Å
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