Database: EMDB / ID: 1246|
|Title||Distribution and three-dimensional structure of AIDS virus envelope spikes.|
|Sample||Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail|
|Source||Simian immunodeficiency virus / virus|
|Map data||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 ).|
|Method||subtomogram averaging, at 32 A resolution|
|Authors||Zhu P / Liu J / Bess J / Chertova E / Lifson JD / Grise H / Ofek GA / Taylor KA / Roux KH|
|Citation||Nature, 2006, 441, 847-852|
|Date||Deposition: Jul 21, 2006 / Header (metadata) release: Jul 25, 2006 / Map release: Jul 25, 2006 / Last update: Jul 21, 2006|
|3D viewer|| / |
Downloads & links
|File||emd_1246.map.gz (map file in CCP4 format, 1459 KB)|
|Projections & slices||Size of images: |
Images are generated by Spider package.
|Voxel size||X=Y=Z: 5.56 A|
CCP4 map header:
Entire Envelope Spike on the surface of SIVmac239 virus with truncated c...
|Entire||Name: 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
|Mass||Theoretical: 450 kDa|
Component #1: protein, Envelope glycoprotein
|Protein||Name: 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
|Mass||Experimental: 450 kDa|
|Source||Species: Simian immunodeficiency virus / virus|
|Sample solution||Buffer solution: PBS|
|Support film||200 mesh Quantifoil R2/1 copper grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Vitrification instrument: Home made plunger|
Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM300FEG/ST / Date: Aug 30, 2004 / Details: Minimum tilt angle was -70|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/A2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 43200 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm|
|Specimen Holder||Holder: Gatan 626 cryoholder / Model: GATAN LIQUID NITROGEN / Tilt Angle: 70 - 70 deg.|
|Camera||Detector: TVIPS TEMCAM-F224 (2k x 2k)|
|Image acquisition||Number of digital images: 80|
|Processing||Method: 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 reconstruction||Algorithm: Weighted backprojection and 3d alignment and averaging|
Software: Protomo / Resolution: 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.
Atomic model buiding
|Modeling #1||Software: 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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