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- EMDB-9566: Human RAD51 presynaptic complex -

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Basic information

Entry
Database: EMDB / ID: 9566
TitleHuman RAD51 presynaptic complex
Map dataHuman RAD51-ssDNA formed presynaptic complex
SampleHuman RAD51 and ssDNA formed presynaptic complex:
Human RAD51 / ssDNADNA / DNA repair protein RAD51 homolog 1 / nucleic-acidNucleic acid / (ligand) x 2
Function / homologyDNA recombination and repair protein RecA-like, ATP-binding domain / HDR through Single Strand Annealing (SSA) / AAA+ ATPase domain / DNA repair Rad51/transcription factor NusA, alpha-helical / DNA recombination/repair protein Rad51 / DNA recombination and repair protein Rad51-like, C-terminal / 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 ...DNA recombination and repair protein RecA-like, ATP-binding domain / HDR through Single Strand Annealing (SSA) / AAA+ ATPase domain / DNA repair Rad51/transcription factor NusA, alpha-helical / DNA recombination/repair protein Rad51 / DNA recombination and repair protein Rad51-like, C-terminal / 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) / 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 / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening / telomere maintenance via recombination / mitotic 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 / site of double-strand break / condensed chromosome / interstrand cross-link repair / nuclear chromosome / condensed nuclear chromosome / meiotic cell cycle / chromatin / double-strand break repair via homologous recombination / microtubule organizing center / cellular response to ionizing radiation / single-stranded DNA binding / PML body / double-stranded DNA binding / nuclear chromosome, telomeric region / protein C-terminus binding / protein homooligomerization / DNA recombination / nuclear chromatin / mitochondrial matrix / cellular response to DNA damage stimulus / DNA repair / 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
Sourcehuman (human)
Methodhelical reconstruction / cryo EM / 4.4 Å resolution
AuthorsXu J / Zhao L
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
Validation ReportPDB-ID: 5h1b

SummaryFull reportAbout validation report
DateDeposition: Oct 8, 2016 / Header (metadata) release: Nov 2, 2016 / Map release: Dec 21, 2016 / Last update: Oct 18, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5h1b
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5h1b
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5h1b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9566.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.31 Å/pix.
= 334.336 Å
256 pix
1.31 Å/pix.
= 334.336 Å
256 pix
1.31 Å/pix.
= 334.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.306 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.014779515 - 0.04188662
Average (Standard dev.)0.00021341213 (0.002159576)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 334.336 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3061.3061.306
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z334.336334.336334.336
α/β/γ90.00090.00090.000
start NX/NY/NZ-2600
NX/NY/NZ264044
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0150.0420.000

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Supplemental data

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Sample components

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Entire Human RAD51 and ssDNA formed presynaptic complex

EntireName: Human RAD51 and ssDNA formed presynaptic complex / Number of components: 7

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Component #1: protein, Human RAD51 and ssDNA formed presynaptic complex

ProteinName: Human RAD51 and ssDNA formed presynaptic complex / Recombinant expression: No
SourceSpecies: human (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG / Vector: pRh51.2

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Component #2: protein, Human RAD51

ProteinName: Human RAD51 / Recombinant expression: No

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Component #3: protein, ssDNA

ProteinName: ssDNADNA / Recombinant expression: No

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Component #4: protein, DNA repair protein RAD51 homolog 1

ProteinName: DNA repair protein RAD51 homolog 1 / Recombinant expression: No
MassTheoretical: 37.008074 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: nucleic-acid, DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

Nucleic-acidName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)
MassTheoretical: 2.692778 kDa

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Component #6: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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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: 15.88 Å / Delta phi: 56.77 deg.
Sample solutionSpecimen conc.: 0.075 mg/ml
Buffer solution: 25mM Tris-HCl, pH 7.5, 50mM KCl, 1mM dithiothreitol, 1mM AMP-PNP and 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: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 40404 / Sampling size: 5 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER, RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1SZP
Chain ID: 1SZP_E
Output model

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