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- EMDB-9568: human RAD51 presynaptic complex -

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Basic information

Entry
Database: EMDB / ID: 9568
Titlehuman RAD51 presynaptic complex
Map data
SampleArrested state in human RAD51-mediated DNA strand exchange:
Function / homologyDNA recombination and repair protein RecA-like, ATP-binding domain / HDR through Single Strand Annealing (SSA) / DNA recombination/repair protein Rad51 / DNA recombination and repair protein Rad51-like, C-terminal / AAA+ ATPase domain / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein RecA, monomer-monomer interface / P-loop containing nucleoside triphosphate hydrolase / Rad51/DMC1/RadA / Rad51 ...DNA recombination and repair protein RecA-like, ATP-binding domain / HDR through Single Strand Annealing (SSA) / DNA recombination/repair protein Rad51 / DNA recombination and repair protein Rad51-like, C-terminal / AAA+ ATPase domain / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein RecA, monomer-monomer interface / P-loop containing nucleoside triphosphate hydrolase / Rad51/DMC1/RadA / Rad51 / RecA family profile 1. / RecA family profile 2. / HDR through Homologous Recombination (HRR) / DNA repair Rad51/transcription factor NusA, alpha-helical / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Transcriptional Regulation by E2F6 / Meiotic recombination / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / telomere maintenance via telomere lengthening / mitotic recombination / telomere maintenance via recombination / single-stranded DNA-dependent ATPase activity / strand invasion / positive regulation of DNA ligation / lateral element / reciprocal meiotic recombination / recombinase activity / DNA unwinding involved in DNA replication / replication fork processing / regulation of double-strand break repair via homologous recombination / negative regulation of G0 to G1 transition / four-way junction DNA binding / DNA polymerase binding / condensed chromosome / site of double-strand break / nuclear chromosome / condensed nuclear chromosome / meiotic cell cycle / microtubule organizing center / double-strand break repair via homologous recombination / chromatin / cellular response to ionizing radiation / interstrand cross-link repair / single-stranded DNA binding / PML body / double-stranded DNA binding / nuclear chromosome, telomeric region / protein homooligomerization / protein C-terminus binding / nuclear chromatin / DNA recombination / mitochondrial matrix / DNA repair / cellular response to DNA damage stimulus / nucleolus / perinuclear region of cytoplasm / mitochondrion / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm / DNA repair protein RAD51 homolog 1
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 14 Å resolution
AuthorsXu J / Zhao L / Xu Y / Zhao W / Sung P / Wang HW
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange.
Authors: Jingfei Xu / Lingyun Zhao / Yuanyuan Xu / Weixing Zhao / Patrick Sung / Hong-Wei Wang
DateDeposition: Oct 8, 2016 / Header (metadata) release: Nov 2, 2016 / Map release: Dec 21, 2016 / Last update: Jan 25, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9568.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.05 Å/pix.
= 420. Å
400 pix
1.05 Å/pix.
= 420. Å
400 pix
1.05 Å/pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.55 (by author), 0.55 (movie #1):
Minimum - Maximum-0.2945868 - 1.0507883
Average (Standard dev.)0.010550541 (0.08465524)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin-200-200-200
Limit199199199
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.2951.0510.011

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Supplemental data

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Sample components

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Entire Arrested state in human RAD51-mediated DNA strand exchange

EntireName: Arrested state in human RAD51-mediated DNA strand exchange
Number of components: 1

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Component #1: protein, Arrested state in human RAD51-mediated DNA strand exchange

ProteinName: Arrested state in human RAD51-mediated DNA strand exchange
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Vector: pRh51.2

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 15.27 Å / Delta phi: 56.4 deg.
Sample solutionSpecimen conc.: 0.075 mg/ml
Buffer solution: 25mM Tris-HCl, pH 7.5, 50mM KCl, 1mM dithiothreitol, 1mM AMP-PNP, 2mM MgCl2
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal), 22500 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80 - 80 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 202 / Sampling size: 14 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 14 Å / Resolution method: FSC 0.5 CUT-OFF

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