[English] 日本語
- EMDB-3876: Cryo-electron tomogram of Marburg virus -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 3876
TitleCryo-electron tomogram of Marburg virus
Map dataA 4x binned representative tomogram of intact Marburg virus virions
SampleLake Victoria marburgvirus - Popp:
SourceLake Victoria marburgvirus - Popp
Methodelectron tomography / cryo EM
AuthorsWan W / Kolesnikova L / Clarke M / Koehler A / Noda T / Becker S / Briggs JAG
CitationJournal: Nature / Year: 2017
Title: Structure and assembly of the Ebola virus nucleocapsid.
Authors: William Wan / Larissa Kolesnikova / Mairi Clarke / Alexander Koehler / Takeshi Noda / Stephan Becker / John A G Briggs
DateDeposition: Sep 13, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Apr 18, 2018

Structure visualization

  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3876.map.gz (map file in CCP4 format, 429665 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
7.12 Å/pix.
= 1780. Å
927 pix
7.12 Å/pix.
= 6600.24 Å
927 pix
7.12 Å/pix.
= 6600.24 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.12 Å
Minimum - Maximum-33.0 - 33.0
Average (Standard dev.)1.9209514 (2.2230742)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 6600.2397 Å / B: 6600.2397 Å / C: 1780.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.127.127.12
M x/y/z927927250
origin x/y/z0.0000.0000.000
length x/y/z6600.2406600.2401780.000
start NX/NY/NZ-128-128-128
MAP C/R/S123
start NC/NR/NS0070
D min/max/mean-33.00033.0001.921

Supplemental data

Sample components

Entire Lake Victoria marburgvirus - Popp

EntireName: Lake Victoria marburgvirus - Popp
Details: Virus was isolated from infected Huh-7 cells. Purified viruses were fixed with paraformaldehyde.
Number of components: 1

Component #1: virus, Lake Victoria marburgvirus - Popp

VirusName: Lake Victoria marburgvirus - Popp / Class: VIRION
Details: Virus was isolated from infected Huh-7 cells. Purified viruses were fixed with paraformaldehyde.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Lake Victoria marburgvirus - Popp

Experimental details

Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Sample solutionBuffer solution: Virus was purified into Dulbecco's modified Eagle's medium (DMEM) with 4% paraformaldehyde
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %

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: 2.9 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4500.0 nm / Energy filter: Gatan Quantum 967 LS / Energy window: -10-10 eV
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image processing

ProcessingMethod: electron tomography / Number of sections: 41
Details: Frames were aligned using K2Align software, based off the MotionCorr algorithm. Tomograms were reconstructed with IMOD, using stripwise CTF-correction and weighted back projection.
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD
CTF correction: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.

About Yorodumi


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 EBI / 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

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

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