[English] 日本語
- EMDB-3464: Cryo-electron tomogram containing mature HIV-1 particles -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 3464
TitleCryo-electron tomogram containing mature HIV-1 particles
SampleHuman immunodeficiency virus 1
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataCryo-electron tomographic reconstruction of wild type mature HIV-1 particles
Methodelectron tomography
AuthorsMattei S / Glass B / Hagen WJH / Kraeusslich H-G / Briggs JAG
CitationScience, 2016, 354, 1434-1437

Science, 2016, 354, 1434-1437 Yorodumi Papers
The structure and flexibility of conical HIV-1 capsids determined within intact virions.
Simone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs

DateDeposition: Nov 10, 2016 / Header (metadata) release: Dec 7, 2016 / Map release: Dec 28, 2016 / Last update: Aug 30, 2017

Structure visualization

  • Simplified surface model
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_3464.map.gz (map file in CCP4 format, 757842 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.78 Å/pix.
= 391.6 Å
928 pix
1.78 Å/pix.
= 1651.84 Å
928 pix
1.78 Å/pix.
= 1651.84 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.78 Å
Contour Level:150 (by author)
Minimum - Maximum-2402.1646 - 1335.3918
Average (Standard dev.)75.47189 (37.212543)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 1651.84 Å / B: 1651.84 Å / C: 391.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z928928220
origin x/y/z0.0000.0000.000
length x/y/z1651.8401651.840391.600
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-2402.1651335.39275.472

Supplemental data

Sample components

Entire Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Number of components: 1

Component #1: virus, Human immunodeficiency virus 1

VirusName: Human immunodeficiency virus 1 / Class: VIRION
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (natural)Host Species: Homo sapiens / human

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 292 K / Humidity: 100 %
Details: 10nm colloidal gold was added to the sample prior to plunge freezing

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Nanoprobe
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 6500 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -66 - 66 deg.
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 3 deg. / Number of sections: 45
Details: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
3D reconstructionSoftware: IMOD

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