[English] 日本語
Yorodumi
- EMDB-9568: human RAD51 presynaptic complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9568
Titlehuman RAD51 presynaptic complex
Map data
SampleArrested state in human RAD51-mediated DNA strand exchange
Function / homology
Function and homology information


response to glucoside / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / mitotic recombination / telomere maintenance via telomere lengthening / telomere maintenance via recombination / replication-born double-strand break repair via sister chromatid exchange / strand invasion ...response to glucoside / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / mitotic recombination / telomere maintenance via telomere lengthening / telomere maintenance via recombination / replication-born double-strand break repair via sister chromatid exchange / strand invasion / positive regulation of DNA ligation / cellular response to cisplatin / cellular response to hydroxyurea / lateral element / recombinase activity / single-stranded DNA helicase activity / reciprocal meiotic recombination / replication fork processing / DNA unwinding involved in DNA replication / regulation of double-strand break repair via homologous recombination / response to ionizing radiation / negative regulation of G0 to G1 transition / DNA-dependent ATPase activity / response to X-ray / DNA polymerase binding / condensed chromosome / condensed nuclear chromosome / nuclear chromosome / regulation of protein phosphorylation / microtubule organizing center / meiotic cell cycle / interstrand cross-link repair / cellular response to ionizing radiation / chromatin / double-strand break repair via homologous recombination / cellular response to gamma radiation / PML body / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / nuclear chromosome, telomeric region / protein C-terminus binding / DNA recombination / mitochondrial matrix / nuclear chromatin / DNA repair / cellular response to DNA damage stimulus / chromatin binding / perinuclear region of cytoplasm / enzyme binding / mitochondrion / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
DNA recombination/repair protein Rad51 / Rad51/DMC1/RadA / P-loop containing nucleoside triphosphate hydrolase / DNA recombination and repair protein RecA-like, ATP-binding domain / DNA recombination and repair protein RecA, monomer-monomer interface / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / DNA repair Rad51/transcription factor NusA, alpha-helical / AAA+ ATPase domain
DNA repair protein RAD51 homolog 1
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 14 Å
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 /
Abstract: The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA-strand exchange mediated by the Rad51 recombinase. In this process, Rad51 assembles on single-stranded DNA (ssDNA) ...The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA-strand exchange mediated by the Rad51 recombinase. In this process, Rad51 assembles on single-stranded DNA (ssDNA) and generates a helical filament that is able to search for and invade homologous double-stranded DNA (dsDNA), thus leading to strand separation and formation of new base pairs between the initiating ssDNA and the complementary strand within the duplex. Here, we used cryo-EM to solve the structures of human RAD51 in complex with DNA molecules, in presynaptic and postsynaptic states, at near-atomic resolution. Our structures reveal both conserved and distinct structural features of the human RAD51-DNA complexes compared with their prokaryotic counterpart. Notably, we also captured the structure of an arrested synaptic complex. Our results provide new insight into the molecular mechanisms of the DNA homology search and strand-exchange processes.
History
DepositionOct 8, 2016-
Header (metadata) releaseNov 2, 2016-
Map releaseDec 21, 2016-
UpdateJan 25, 2017-
Current statusJan 25, 2017Processing site: PDBj / Status: Released

-
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

-
Map

FileDownload / File: emd_9568.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å
1.05 Å/pix.
x 400 pix.
= 420. Å
1.05 Å/pix.
x 400 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 LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-0.2945868 - 1.0507883
Average (Standard dev.)0.010550541 (±0.08465524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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

-
Supplemental data

-
Sample components

-
Entire Arrested state in human RAD51-mediated DNA strand exchange

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

-
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
MassTheoretical: 26.12 MDa
SourceSpecies: Homo sapiens (human)

-
Experimental details

-
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 %

-
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: 22500.0 X (nominal), 22500.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (80.0 - 80.0 K)
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

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

-
Image processing

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

-
Atomic model buiding

Modeling #1Refinement space: REAL

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more