+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2779 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Electron microscopy of human BRCA2 tumour suppressor protein | |||||||||
Map data | Reconstruction of active full-length human BRCA2 dimer | |||||||||
Sample |
| |||||||||
Keywords | tumour suppressor / DNA double-strand break repair / homologous recombination / negative stain | |||||||||
Function / homology | Function and homology information 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) / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination / histone H4 acetyltransferase activity ...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) / 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 / response to UV-C / DNA repair complex / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / 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 / response to gamma radiation / cellular response to ionizing radiation / nucleotide-excision repair / double-strand break repair via homologous recombination / brain development / HDR through Homologous Recombination (HRR) / Meiotic recombination / cellular senescence / double-strand break repair / single-stranded DNA binding / spermatogenesis / protease binding / 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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 18.5 Å | |||||||||
Authors | Shahid T / Soroka J / Kong EH / Malivert L / McIlwraith MJ / Pape T / West SC / Zhang X | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2014 Title: Structure and mechanism of action of the BRCA2 breast cancer tumor suppressor. Authors: Taha Shahid / Joanna Soroka / Eric Kong / Laurent Malivert / Michael J McIlwraith / Tillman Pape / Stephen C West / Xiaodong Zhang / Abstract: Mutations in BRCA2 increase susceptibility to breast, ovarian and prostate cancers. The product of human BRCA2, BRCA2 protein, has a key role in the repair of DNA double-strand breaks and interstrand ...Mutations in BRCA2 increase susceptibility to breast, ovarian and prostate cancers. The product of human BRCA2, BRCA2 protein, has a key role in the repair of DNA double-strand breaks and interstrand cross-links by RAD51-mediated homologous recombination. Here, we present a biochemical and structural characterization of full-length (3,418 amino acid) BRCA2, alone and in complex with RAD51. We show that BRCA2 facilitates nucleation of RAD51 filaments at multiple sites on single-stranded DNA. Three-dimensional EM reconstructions revealed that BRCA2 exists as a dimer and that two oppositely oriented sets of RAD51 molecules bind the dimer. Single-stranded DNA binds along the long axis of BRCA2, such that only one set of RAD51 monomers can form a productive complex with DNA and establish filament formation. Our data define the molecular mechanism by which this tumor suppressor facilitates RAD51-mediated homologous-recombinational repair. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2779.map.gz | 445.3 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2779-v30.xml emd-2779.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2779_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_2779.png emd_2779_1.png | 52.5 KB 49.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2779 | HTTPS FTP |
-Validation report
Summary document | emd_2779_validation.pdf.gz | 218.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2779_full_validation.pdf.gz | 217.7 KB | Display | |
Data in XML | emd_2779_validation.xml.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2779 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2779 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2779.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of active full-length human BRCA2 dimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Full-length human BRCA2 protein
Entire | Name: Full-length human BRCA2 protein |
---|---|
Components |
|
-Supramolecule #1000: Full-length human BRCA2 protein
Supramolecule | Name: Full-length human BRCA2 protein / type: sample / ID: 1000 / Details: The sample was very dilute, ~0.0025 mg/ml. / Oligomeric state: Homodimer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 800 KDa / Theoretical: 768 KDa / Method: Scanning transmission electron microscopy |
-Macromolecule #1: Breast cancer type 2 susceptibility protein
Macromolecule | Name: Breast cancer type 2 susceptibility protein / type: protein_or_peptide / ID: 1 / Name.synonym: BRCA2 / Number of copies: 2 / Oligomeric state: Homodimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
Molecular weight | Theoretical: 384 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HeLa |
Sequence | UniProtKB: Breast cancer type 2 susceptibility protein / InterPro: Breast cancer type 2 susceptibility protein |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE Details: Grid with adsorbed protein was negatively stained with 2% uranyl acetate solution before being blotted and air dried. |
---|---|
Grid | Details: TAAB copper 300-mesh continuous carbon grid, glow discharged in air. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy #1
Microscopy ID | 1 |
---|---|
Microscope | FEI/PHILIPS CM200FEG |
Date | Mar 14, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Electron microscopy #2
Microscopy ID | 2 |
---|---|
Microscope | FEI/PHILIPS CM200FEG |
Date | Mar 16, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Electron microscopy #3
Microscopy ID | 3 |
---|---|
Microscope | FEI/PHILIPS CM200FEG |
Date | Mar 21, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Electron microscopy #4
Microscopy ID | 4 |
---|---|
Microscope | FEI/PHILIPS CM200FEG |
Date | Mar 22, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |