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- EMDB-2779: Electron microscopy of human BRCA2 tumour suppressor protein -

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Basic information

Entry
Database: EMDB / ID: EMD-2779
TitleElectron microscopy of human BRCA2 tumour suppressor protein
Map dataReconstruction of active full-length human BRCA2 dimer
Sample
  • Sample: Full-length human BRCA2 protein
  • Protein or peptide: Breast cancer type 2 susceptibility protein
Keywordstumour 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 / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / lateral element / histone H4 acetyltransferase activity / histone H3 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 / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / lateral element / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA repair complex / oocyte maturation / response to UV-C / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / Impaired BRCA2 binding to RAD51 / hematopoietic stem cell proliferation / female gonad development / male meiosis I / centrosome duplication / Presynaptic phase of homologous DNA pairing and strand exchange / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / positive regulation of mitotic cell cycle / secretory granule / regulation of cytokinesis / cellular response to ionizing radiation / response to gamma radiation / nucleotide-excision repair / double-strand break repair via homologous recombination / brain development / Meiotic recombination / HDR through Homologous Recombination (HRR) / cellular senescence / double-strand break repair / single-stranded DNA binding / protease binding / spermatogenesis / 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
BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 ...BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 / BRCA2 TR2 domain / Tower / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Breast cancer type 2 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 18.5 Å
AuthorsShahid T / Soroka J / Kong EH / Malivert L / McIlwraith MJ / Pape T / West SC / Zhang X
CitationJournal: 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
DepositionSep 3, 2014-
Header (metadata) releaseSep 17, 2014-
Map releaseOct 8, 2014-
UpdateOct 8, 2014-
Current statusOct 8, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0921
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0921
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2779.png

emd_2779_1.png

Downloads & links

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Map

FileDownload / File: emd_2779.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of active full-length human BRCA2 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0921 / Movie #1: 0.0921
Minimum - Maximum-0.22995593 - 0.58755279
Average (Standard dev.)0.00190962 (±0.02442834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.523.523.52
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z450.560450.560450.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.2300.5880.002

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Supplemental data

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Sample components

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Entire : Full-length human BRCA2 protein

EntireName: Full-length human BRCA2 protein
Components
  • Sample: Full-length human BRCA2 protein
  • Protein or peptide: Breast cancer type 2 susceptibility protein

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Supramolecule #1000: Full-length human BRCA2 protein

SupramoleculeName: 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 weightExperimental: 800 KDa / Theoretical: 768 KDa / Method: Scanning transmission electron microscopy

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Macromolecule #1: Breast cancer type 2 susceptibility protein

MacromoleculeName: 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 weightTheoretical: 384 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HeLa
SequenceUniProtKB: Breast cancer type 2 susceptibility protein / InterPro: Breast cancer type 2 susceptibility protein

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE
Details: Grid with adsorbed protein was negatively stained with 2% uranyl acetate solution before being blotted and air dried.
GridDetails: TAAB copper 300-mesh continuous carbon grid, glow discharged in air.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI/PHILIPS CM200FEG
DateMar 14, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI/PHILIPS CM200FEG
DateMar 16, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Electron microscopy #3

Microscopy ID3
MicroscopeFEI/PHILIPS CM200FEG
DateMar 21, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Electron microscopy #4

Microscopy ID4
MicroscopeFEI/PHILIPS CM200FEG
DateMar 22, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsThe particles were selected manually in EMAN2.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.5 Å / Resolution method: OTHER / Software - Name: IMAGIC-5, Tigris
Details: Final maps were calculated after a round of projection matching.
Number images used: 8873
Final angle assignmentDetails: IMAGIC: 0 < Beta < 180 degrees, -90 < Gamma < 90 degrees
Final two d classificationNumber classes: 568
FSC plot (resolution estimation)

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