REL PDBe PDBe PDBe 2006-04-18 2006-04-18 2006-09-05 2013-12-11 Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ. Zanetti G Briggs JAG Gruenewald K Sattentau Q Fuller SD Zanetti G Briggs JA Grunewald K Sattentau QJ Fuller SD Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ. PLOS PATHOG. 2 e83 e83 2006 16933990 doi:10.1371/journal.ppat.0020083 Simian Immunodeficiency Virus mne Envelope Complex Simian Immunodeficiency Virus mne Envelope Complex
The envelope complex wasn't purified but it was analysed on the virus
trimer of Gp120 and trimer of Gp41 and membrane 3 0.500 0.500 sum of individual components is an underestimate due to the presence of the membrane viral envelope
viral membrane
viral envelope Macaca nemestrina VERTEBRATES membrane 1200 VIRION STRAIN true false viral membrane gp120 Simian immunodeficiency virus SIVMneCL8 SIVmne HuT 78 viral membrane 0.120 0.120
trimeric
3 trimer false gp41 Simian immunodeficiency virus SIVMneCL8 SIVmne HuT 78 viral membrane 0.041 0.041
trimeric
3 trimer false subtomogramAveraging particle 1 7.2
PBS
 NEGATIVE
Samples were mixed with BSA adsorbed 10 nm colloidal gold and vitrified for cryoelectron microscopy.
holey carbon film
 ETHANE HOMEMADE PLUNGER
Vitrification instrument: home built
blot for two seconds before plunging FEI/PHILIPS CM300FEG/ST FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 0.4 0.6 27500.0 GATAN LIQUID NITROGEN 77 GATAN GIF 2002 0.0 20.0
We collected a tilt series
2005-10-01 GENERIC GATAN 30 3 57 eucentric 69.0 63
Average number of projections used in the 3D reconstructions: 2986.
OTHER 28.0 FSC 0.5 CUT-OFF TOM
envelope complexes were averaged to give a final map of 28A resolution as determined by FSC at 0.5 cut-off.
 emd_1216.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 63 63 63 -31 -31 -31 63 63 63 344.61 344.61 344.61 90 90 90 X Y Z -15307.0 20000.0 117.353999999999999 3616.260000000000218 5.47 5.47 5.47 8160.0 This is the volume of the averaged SIV envelope complex
::::EMDATABANK.org::::EMD-1216::::
 2BF1 A RIGID BODY FIT URO
PDBEntryID_givenInChain. Protocol: rigid body. The gp120 monomer was manually fitted and three-fold symmetry was imposed during fitting with URO
quadratic misfit RECIPROCAL emd_1216_msk_2.map emd_1216_msk_2.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 63 63 63 -31 -31 -31 63 63 63 344.61 344.61 344.61 90.0 90.0 90.0 X Y Z -1.081926 0.82805485 -0.0019963253 0.13918164 5.47 5.47 5.47 Protein with the mask applied is the simple multiplication of the spike protein map (emd_1216.map) with the mask (emd_1216_mask_1.map)
::::EMDATABANK.org::::EMD-1216::::MASK:1::::
 emd_1216_msk_1.map emd_1216_msk_1.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 63 63 63 -31 -31 -31 63 63 63 344.61 344.61 344.61 90.0 90.0 90.0 X Y Z -0. 1.0 0.17247473 0.35111478 5.47 5.47 5.47 The mask for the averaged SIV envelope complex
::::EMDATABANK.org::::EMD-1216::::MASK:2::::