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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: EMD-1246
TitleDistribution and three-dimensional structure of AIDS virus envelope spikes.
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 ).
Sample
  • Sample: Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
  • Protein or peptide: Envelope glycoprotein
Biological speciesSimian immunodeficiency virus
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsZhu P / Liu J / Bess J / Chertova E / Lifson JD / Grise H / Ofek GA / Taylor KA / Roux KH
CitationJournal: Nature / 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 /
Abstract: Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are ...Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are known, the structure and distribution of native Env spikes on virions is obscure. We applied cryoelectron microscopy tomography to define ultrastructural details of spikes. Virions of wild-type human immunodeficiency virus 1 (HIV-1) and a mutant simian immunodeficiency virus (SIV) had approximately 14 and approximately 73 spikes per particle, respectively, with some clustering of HIV-1 spikes. Three-dimensional averaging showed that the surface glycoprotein (gp120) 'head' of each subunit of the trimeric SIV spike contains a primary mass, with two secondary lobes. The transmembrane glycoprotein 'stalk' of each trimer is composed of three independent legs that project obliquely from the trimer head, tripod-like. Reconciling available atomic structures with the three-dimensional whole spike density map yields insights into the orientation of Env spike structural elements and possible structural bases of their functions.
History
DepositionJul 21, 2006-
Header (metadata) releaseJul 25, 2006-
Map releaseJul 25, 2006-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1246.gif

Downloads & links

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Map

FileDownload / File: emd_1246.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D 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 ).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.56 Å/pix.
x 72 pix.
= 400.32 Å		5.56 Å/pix.
x 72 pix.
= 400.32 Å		5.56 Å/pix.
x 72 pix.
= 400.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.56 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.34 / Movie #1: 2.65
Minimum - Maximum-7.62291 - 12.339600000000001
Average (Standard dev.)-0.0000000284499 (±0.901928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-36-36-36
Dimensions727272
Spacing727272
CellA=B=C: 400.32 Å
α=β=γ: 90 °

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
Components
  • Sample: Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
  • Protein or peptide: Envelope glycoprotein

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Supramolecule #1000: Envelope Spike on the surface of SIVmac239 virus with truncated c...

SupramoleculeName: Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
type: sample / ID: 1000
Details: The virus was AT-2 treated to eliminate the infectivity.
Oligomeric state: Trimer / Number unique components: 1
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: gp120, gp41
Details: The spike consists of 3 copies of gp120 and gp41 ecto domain to form a trimer
Oligomeric state: trimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightExperimental: 450 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferDetails: PBS
GridDetails: 200 mesh Quantifoil R2/1 copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
DetailsMinimum tilt angle was -70
DateAug 30, 2004
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Number real images: 80 / Average electron dose: 60 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 43200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder: Gatan 626 cryoholder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 70 ° / Tilt series - Axis1 - Max angle: 70 °

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Image processing

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.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: Protomo
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 ...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 1

Initial model
PDB IDChain

2bf1

chain_id: A

1tji

chain_id: P

1tzg

chain_id: P
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. 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.
RefinementProtocol: RIGID BODY FIT

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