REL PDBe PDBe PDBe 2006-07-21 2006-07-25 2006-07-25 2012-10-31 Distribution and three-dimensional structure of AIDS virus envelope spikes. Zhu P Liu J Bess J Chertova E Lifson JD Grise H Ofek GA Taylor KA Roux KH Zhu P Liu J Bess J Jr Chertova E Lifson JD Grise H Ofek GA Taylor KA Roux KH Distribution and three-dimensional structure of AIDS virus envelope spikes. NATURE 441 847 852 2006 16728975 doi:10.1038/nature04817 Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
The virus was AT-2 treated to eliminate the infectivity.
Trimer 1 0.45 Envelope glycoprotein Simian immunodeficiency virus 0.45
The spike consists of 3 copies of gp120 and gp41 ecto domain to form a trimer
trimer false subtomogramAveraging
PBS
200 mesh Quantifoil R2/1 copper grid
 ETHANE HOMEMADE PLUNGER
Vitrification instrument: Home made plunger
 FEI/PHILIPS CM300FEG/ST FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 4.0 6.0 43200.0 GATAN LIQUID NITROGEN
Minimum tilt angle was -70
2004-08-30 TVIPS TEMCAM-F224 (2k x 2k) 80 60 Gatan 626 cryoholder 70 70
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.
OTHER 32.0 OTHER Protomo
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.
 emd_1246.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 72 72 72 -36 -36 -36 72 72 72 400.32 400.32 400.32 90 90 90 X Y Z -7.62291 12.339600000000001 -0.0000000284499 0.901928 5.56 5.56 5.56 1.34 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 ).
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 2BF1 A 1TJI P 1TZG P RIGID BODY FIT Chimera
PDBEntryID_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.
emd_4910.tif