EMDB-1246: Distribution and three-dimensional structure of AIDS v...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1246
Title	Distribution and three-dimensional structure of AIDS virus envelope spikes.
Map	3D 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 ).
Sample	Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
Authors	Zhu P, Liu J, Bess J, Chertova E, Lifson JD, Grise H, Ofek GA, Taylor KA, Roux KH
Date	Deposition: 2006-07-21, Header release: 2006-07-25, Map release: 2006-07-25, Last update: 2012-10-31
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 2.65, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 2.65, Made by UCSF CHIMERA
Supplemental images	1246.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1247 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1852 PDB-4a7f PDB-4a7l PDB-4a7h List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nature, Vol. 441, Issue 7095, Page 847-52, Year 2006
Title	Distribution and three-dimensional structure of AIDS virus envelope spikes.
Authors	Ping 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.
Keywords	Acquired 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
Links	DOI: 10.1038/nature04817, PubMed: 16728975

Map

File

EMD-1246.map ( map file in CCP4 format, 1494 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	1.34, 2.65 (movie #1):
Minimum - Maximum:	-7.62291 - 12.3396
Average (Standard dev.):	-2.84499e-08 (0.901928)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	72	72	72
Origin	-36	-36	-36
Limit	35	35	35
Spacing	72	72	72

Unit Cell

A= B= C: 400.32 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 5.56 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	5.56	5.56	5.56
M x/y/z	72	72	72
origin x/y/z	0.000	0.000	0.000
length x/y/z	400.320	400.320	400.320
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-64	-64	-64
NX/NY/NZ	128	128	128
MAP C/R/S	1	2	3
start NC/NR/NS	-36	-36	-36
NC/NR/NS	72	72	72
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-7.623	12.340	-0.000

Annotation Details

3D 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	1246.gif

Sample
Name	Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
Number of Components	1
Oligomeric State	Trimer
Theoretical Mass	0.45MDa
Details	The virus was AT-2 treated to eliminate the infectivity.
Component #1: protein - gp120, gp41
Scientific name	Envelope glycoprotein
Common Name	gp120, gp41
Experimental Mass	0.45 MDa
Details	The spike consists of 3 copies of gp120 and gp41 ecto domain to form a trimer
Oligomeric Details	trimer
Scientific Name of Species	Simian immunodeficiency virus
NCBI taxonomy	11723
Recombinant expression	No

Experiment
Sample Preparation
Specimen Support Details	200 mesh Quantifoil R2/1 copper grid
Buffer	Details: PBS
Vitrification
Cryogen Name	ETHANE
Instrument	HOMEMADE PLUNGER
Details	Vitrification instrument: Home made plunger
Imaging
Microscope	FEI/PHILIPS CM300FEG/ST
Date	2004-08-30
Details	Minimum tilt angle was -70
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	60 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Calibrated: 43200
Imaging Mode	BRIGHT FIELD
Defocus	4000 nm - 6000 nm
Specimen Holder
Holder	Gatan 626 cryoholder
Model	GATAN LIQUID NITROGEN
Tilt Angle	70 degrees - 70 degrees
Camera
Detector	Tietz Tem-Cam F224 slow scan CCD camera
Image Acquisition
Number of Digital Images	80

Processing
Method	subtomogram averaging
3D reconstruction
Algorithm	Weighted backprojection and 3d alignment and averaging
Software	Protomo
Resolution By Author	32 A
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.
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.
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Software	Chimera
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.
PDB Entry ID	2BF1, 1TJI, 1TZG PDB-2bf1 PDB-1tji PDB-1tzg
PDB Chain ID	2BF1_A, 1TJI_P, 1TZG_P

Download

Data from EMDB

Header (meta data in XML format)

emd-1246.xml (8.3 KB)

Map data

emd_1246.map.gz (1.3 MB)

Images

1246.gif (57.6 KB)

FTP directory

ftp://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