|Entry||Database: EMDB / ID: 9568|
|Title||human RAD51 presynaptic complex|
|Sample||Arrested state in human RAD51-mediated DNA strand exchange:|
|Function / homology||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 ...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
|Source||Homo sapiens (human)|
|Method||helical reconstruction / cryo EM / 14 Å resolution|
|Authors||Xu J / Zhao L / Xu Y / Zhao W / Sung P / Wang HW|
|Citation||Journal: 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
|Date||Deposition: Oct 8, 2016 / Header (metadata) release: Nov 2, 2016 / Map release: Dec 21, 2016 / Last update: Jan 25, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9568.map.gz (map file in CCP4 format, 256001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.05 Å|
CCP4 map header:
-Entire Arrested state in human RAD51-mediated DNA strand exchange
|Entire||Name: 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
|Protein||Name: Arrested state in human RAD51-mediated DNA strand exchange|
Recombinant expression: No
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)|
|Specimen||Specimen state: filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 15.27 Å / Delta phi: 56.4 deg.|
|Sample solution||Specimen conc.: 0.075 mg/ml|
Buffer solution: 25mM Tris-HCl, pH 7.5, 50mM KCl, 1mM dithiothreitol, 1mM AMP-PNP, 2mM MgCl2
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 22500 X (nominal), 22500 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2500 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80 - 80 K)|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 202 / Sampling size: 14 microns|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 14 Å / Resolution method: FSC 0.5 CUT-OFF|
-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.
-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
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
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