[English] 日本語
- EMDB-7477: Cdc48 in the presence of ADP -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 7477
TitleCdc48 in the presence of ADP
Map dataCdc48-Npl4 complex in the presence of ATP-gamma-S
SourceChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / 7.2 Å resolution
AuthorsKim KH / Bodnar NO
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport
DateDeposition: Feb 22, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Jul 4, 2018 / Last update: Jul 25, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_7477.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.24 Å/pix.
= 317.44 Å
256 pix
1.24 Å/pix.
= 317.44 Å
256 pix
1.24 Å/pix.
= 317.44 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.12085942 - 0.15911137
Average (Standard dev.)0.00046948393 (0.006046737)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 317.44 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z317.440317.440317.440
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1210.1590.000

Supplemental data

Sample components

Entire Cdc48

EntireName: Cdc48 / Number of components: 2

Component #1: cellular-component, Cdc48

Cellular-componentName: Cdc48 / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

Component #2: protein, Cdc48

ProteinName: Cdc48 / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.04 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1600.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1628

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 9751
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

About Yorodumi


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

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

Read more


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