[English] 日本語
- EMDB-5124: Cryo-EM of Rift Valley fever virus -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 5124
TitleCryo-EM of Rift Valley fever virus
Keywordscryo-electron microscopy / single particle averaging / Rift valley fever / bunyaviridae / inter-capsomer contacts
SampleRift Valley fever virus, RVFV vaccine strain MP-12
SourceRift Valley fever virus / virus / RVFV
Map datathis is RVFV map in 2-fold orientation
Methodsingle particle (icosahedral) reconstruction, at 27 Å resolution
AuthorsSherman MB / Freiberg AN / Holbrook AM / Watowich SJ
CitationVirology, 2009, 387, 11-15

primary. Virology, 2009, 387, 11-15 Yorodumi Papers
Single-particle cryo-electron microscopy of Rift Valley fever virus.
Michael B Sherman / Alexander N Freiberg / Michael R Holbrook / Stanley J Watowich

1. J.VIROL., 2008, 82, 10341-10348
Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography
Freiberg AN / Sherman MB / Morais MC / Holbrook MR / Watowich SJ

DateDeposition: Jul 20, 2009 / Header (metadata) release: Jul 24, 2009 / Map release: Jul 24, 2009 / Last update: Jul 8, 2011

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 7.3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 7.3
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5124.map.gz (map file in CCP4 format, 358337 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
451 pix
3 Å/pix.
= 1353. Å
451 pix
3 Å/pix.
= 1353. Å
451 pix
3 Å/pix.
= 1353. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3 Å
Contour Level:6 (by author), 7.3 (movie #1):
Minimum - Maximum-26.2832 - 37.4125
Average (Standard dev.)0.675954 (6.08815)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1353 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z451451451
origin x/y/z0.0000.0000.000
length x/y/z1353.0001353.0001353.000
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-225-225-225
D min/max/mean-26.28337.4120.676

Supplemental data

Sample components

Entire Rift Valley fever virus, RVFV vaccine strain MP-12

EntireName: Rift Valley fever virus, RVFV vaccine strain MP-12 / Details: monodisperse sample / Number of components: 8 / Oligomeric State: single virions

Component #1: virus, Rift Valley fever virus

VirusName: Rift Valley fever virus / a.k.a: RVFV / Class: VIRION / Details: 100 nm particles / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Rift Valley fever virus / virus / RVFV
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA / pH: 7.2
Support film200 mesh copper Qauntifoil grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 95 K / Humidity: 80 % / Method: blot 2 sec before plunging / Details: Vitrification instrument: pneumatic plunger

Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Nov 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (nominal), 40200 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3700 nm / Energy filter: omega / Energy window: 0-20 eV
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 99 K ( 99 - 99 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 93 / Sampling size: 14 microns / Bit depth: 16

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 108 / Number of class averages: 1 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: PFT / Software: PFT / CTF correction: Each particle / Details: Final map calculated from 108 particles / Resolution: 27 Å / Resolution method: FSC

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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)

Read more


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