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Distribution and three-dimensional structure of AIDS virus envelope spikes.

by subtomogram averaging, at 32 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.65, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2.65, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1246
TitleDistribution and three-dimensional structure of AIDS virus envelope spikes.
Map3D 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 ).
SampleEnvelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
AuthorsZhu P, Liu J, Bess J, Chertova E, Lifson JD, Grise H, Ofek GA, Taylor KA, Roux KH
DateDeposition: 2006-07-21, Header release: 2006-07-25, Map release: 2006-07-25, Last update: 2012-10-31
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.65, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2.65, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleNature, Vol. 441, Issue 7095, Page 847-52, Year 2006
TitleDistribution and three-dimensional structure of AIDS virus envelope spikes.
AuthorsPing Zhu, Jun Liu, Julian Bess, Elena Chertova, Jeffrey D Lifson, Henry Grisé, Gilad A Ofek, Kenneth A Taylor, Kenneth H Roux
Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
KeywordsAcquired Immunodeficiency Syndrome (virology), Cryoelectron Microscopy, Glycoproteins (chemistry), HIV Envelope Protein gp120 (chemistry), HIV-1 (chemistry), Ligands, Models, Molecular, Protein Structure, Quaternary, Protein Subunits (chemistry), Simian immunodeficiency virus (chemistry), Structure-Activity Relationship, Tomography
LinksDOI: 10.1038/nature04817, PubMed: 16728975
Map
Fileemd_1246.map.gz ( map file in CCP4 format, 1459 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
72 pix
5.56 A/pix
= 400.32 A
72 pix
5.56 A/pix
= 400.32 A
72 pix
5.56 A/pix
= 400.32 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.34, 2.65 (movie #1):
Minimum - Maximum: -7.62291 - 12.3396
Average (Standard dev.): -2.84499e-08 (0.901928)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions727272
Origin-36-36-36
Limit353535
Spacing727272
Unit CellA= B= C: 400.32 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5.56 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-36-36-36
NC/NR/NS727272
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-7.62312.340-0.000
Annotation Details3D 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 ).
Supplement
Images
Images
Sample
NameEnvelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
Number of Components1
Oligomeric StateTrimer
Theoretical Mass0.45MDa
DetailsThe virus was AT-2 treated to eliminate the infectivity.
Component #1: protein - gp120, gp41
Scientific nameEnvelope glycoprotein
Common Namegp120, gp41
Experimental Mass0.45 MDa
DetailsThe spike consists of 3 copies of gp120 and gp41 ecto domain to form a trimer
Oligomeric Detailstrimer
Scientific Name of SpeciesSimian immunodeficiency virus
NCBI taxonomy11723
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Support Details200 mesh Quantifoil R2/1 copper grid
BufferDetails: PBS
Vitrification
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
DetailsVitrification instrument: Home made plunger
Imaging
MicroscopeFEI/PHILIPS CM300FEG/ST
Date2004-08-30
DetailsMinimum tilt angle was -70
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose60 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationCalibrated: 43200
Imaging ModeBRIGHT FIELD
Defocus4000 nm - 6000 nm
Specimen Holder
HolderGatan 626 cryoholder
ModelGATAN LIQUID NITROGEN
Tilt Angle70 degrees - 70 degrees
Camera
DetectorTVIPS TEMCAM-F224 (2k x 2k)
Image Acquisition
#1
Number of Digital Images80
Processing
Methodsubtomogram averaging
3D reconstruction
AlgorithmWeighted backprojection and 3d alignment and averaging
SoftwareProtomo
Resolution By Author32 A
Resolution MethodEstimated first node in the CTF
DetailsThe 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.
Subtomogram Averaging
DetailsThe 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.
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
SoftwareChimera
DetailsThe 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.
PDB Entry ID2BF1, 1TJI, 1TZG
PDB Chain ID2BF1_A, 1TJI_P, 1TZG_P
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Data from EMDB
Header (meta data in XML format)emd-1246.xml (8.3 KB)
Map dataemd_1246.map.gz (1.3 MB)
Images1246.gif (57.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1246
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 19.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 19.8 KB