[English] 日本語
- EMDB-1246: Distribution and three-dimensional structure of AIDS virus envelo... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1246
TitleDistribution and three-dimensional structure of AIDS virus envelope spikes.
SampleEnvelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
SourceSimian immunodeficiency virus / virus / サル免疫不全ウイルス
Map data3D map of SIVmac239 envelope spike. It is the 3D averaged volume of all spikes including both "top/bottom view" and "side view" subsets (supplementary method of the reference). Author's threshold 2.65. It should be loaded together with the associated viral membrane map (SIVmac239_Vir_memb.map, EMD-1247, author's threshold 2.25 ).
Methodsubtomogram averaging, at 32 Å resolution
AuthorsZhu P / Liu J / Bess J / Chertova E / Lifson JD / Grise H / Ofek GA / Taylor KA / Roux KH
CitationNature, 2006, 441, 847-852

Nature, 2006, 441, 847-852 Yorodumi Papers
Distribution and three-dimensional structure of AIDS virus envelope spikes.
Ping Zhu / Jun Liu / Julian Bess / Elena Chertova / Jeffrey D Lifson / Henry Grisé / Gilad A Ofek / Kenneth A Taylor / Kenneth H Roux

DateDeposition: Jul 21, 2006 / Header (metadata) release: Jul 25, 2006 / Map release: Jul 25, 2006 / Last update: Oct 31, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2.65
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.65
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1246.map.gz (map file in CCP4 format, 1459 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
72 pix
5.56 Å/pix.
= 400.32 Å
72 pix
5.56 Å/pix.
= 400.32 Å
72 pix
5.56 Å/pix.
= 400.32 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.56 Å
Contour Level:1.34, 2.65 (movie #1):
Minimum - Maximum-7.62291 - 12.3396
Average (Standard dev.)-2.84499e-08 (0.901928)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 400.32 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.565.565.56
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z400.320400.320400.320
start NX/NY/NZ-64-64-64
MAP C/R/S123
start NC/NR/NS-36-36-36
D min/max/mean-7.62312.340-0.000

Supplemental data

Sample components

Entire Envelope Spike on the surface of SIVmac239 virus with truncated c...

EntireName: Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
Details: The virus was AT-2 treated to eliminate the infectivity.
Number of components: 1 / Oligomeric State: Trimer
MassTheoretical: 450 kDa

Component #1: protein, Envelope glycoprotein

ProteinName: Envelope glycoprotein / a.k.a: gp120, gp41 / Oligomeric Details: trimer
Details: The spike consists of 3 copies of gp120 and gp41 ecto domain to form a trimer
Recombinant expression: No
MassExperimental: 450 kDa
SourceSpecies: Simian immunodeficiency virus / virus / サル免疫不全ウイルス

Experimental details

Sample preparation

Sample solutionBuffer solution: PBS
Support film200 mesh Quantifoil R2/1 copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Vitrification instrument: Home made plunger

Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/ST / Date: Aug 30, 2004 / Details: Minimum tilt angle was -70
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 43200 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm
Specimen HolderHolder: Gatan 626 cryoholder / Model: GATAN LIQUID NITROGEN / Tilt Angle: 70 - 70 deg.
CameraDetector: TVIPS TEMCAM-F224 (2k x 2k)

Image acquisition

Image acquisitionNumber of digital images: 80

Image processing

ProcessingMethod: subtomogram averaging
Details: The tomographic tilt angle increment was determined by cosine rule, i.e., ~2-3 degrees increment around low tilt angles and <1 degree increment in the high tilt angles. Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 2.
3D reconstructionAlgorithm: Weighted backprojection and 3d alignment and averaging
Software: Protomo / Resolution: 32 Å / Resolution method: Estimated first node in the CTF
Details: The resolution of the final averaged map, determined by Fourier shell correlation (based on a cutoff value of 0.5) is 2.5 nm and, after low pass filtering to the estimated first node in the contrast transfer function, 3.2 nm.

Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body
Details: The gp120 core and 2F5 and 4E10 peptides structure were fittted by manual docking using program chimera and then applied 3-fold symmetry around Z axis.
Input PDB model: 2BF1, 1TJI, 1TZG
Chain ID: 2BF1_A, 1TJI_P, 1TZG_P

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