[English] 日本語
Yorodumi
- EMDB-9567: Human RAD51 post-synaptic complexes -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 9567
TitleHuman RAD51 post-synaptic complexes
SampleHuman RAD51 post-synaptic complex
Map data
Methodhelical reconstruction, at 4.5 Å resolution
AuthorsXu J / Zhao L
CitationNat. Struct. Mol. Biol., 2017, 24, 40-46

Nat. Struct. Mol. Biol., 2017, 24, 40-46 StrPapers
Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange.
Jingfei Xu / Lingyun Zhao / Yuanyuan Xu / Weixing Zhao / Patrick Sung / Hong-Wei Wang

Validation ReportPDB-ID: 5h1c

SummaryFull reportAbout validation report
DateDeposition: Oct 28, 2016 / Header (metadata) release: Nov 2, 2016 / Map release: Dec 21, 2016 / Last update: Jan 25, 2017

-
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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5h1c
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5h1c
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_9567.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 package.

Voxel sizeX=Y=Z: 1.306 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.018787928 - 0.051937886
Average (Standard dev.)0.00038559092 (0.0028562339)
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-0.0190.0520.000

-
Supplemental data

-
Sample components

+
Entire Human RAD51 post-synaptic complex

EntireName: Human RAD51 post-synaptic complex / Number of components: 9

+
Component #1: protein, Human RAD51 post-synaptic complex

ProteinName: Human RAD51 post-synaptic complex / Recombinant expression: No
Source (engineered)Expression System: Human / mammal / Vector: 1

+
Component #2: protein, Human RAD51

ProteinName: Human RAD51 / Recombinant expression: No

+
Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No

+
Component #4: protein, DNA

ProteinName: DNA / Recombinant expression: No

+
Component #5: 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

+
Component #6: 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

+
Component #7: nucleic-acid, DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

Nucleic-acidName: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)
MassTheoretical: 2.773904 kDa

+
Component #8: ligand, MAGNESIUM ION

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

+
Component #9: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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

-
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 15.8 Å / Delta phi: 56.18 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 %

-
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
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2500 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 528 / Sampling size: 5 microns

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER, RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

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

+
About Yorodumi

-
News

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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

Read more

-
Yorodumi

Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more