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

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Basic information

Entry
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 StrPapers
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

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Structure visualization

Movie
  • 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:
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Slabnear <=> far

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Supplemental images

Downloads & links

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Map

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

Image control

Size
Brightness
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Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions727272
Origin-36-36-36
Limit353535
Spacing727272
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
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-36-36-36
NC/NR/NS727272
D min/max/mean-7.62312.340-0.000

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Supplemental data

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Sample components

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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

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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

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Experimental details

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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

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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)

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Image acquisition

Image acquisitionNumber of digital images: 80

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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.

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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

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