REL PDBe PDBe PDBe 2013-10-11 2013-10-30 2013-10-30 2014-04-16 Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy Bartesaghi A Merk A Borgnia MJ Milne JLS Subramaniam S HIV-1 envelope glycoprotein, SOSIP gp140 trimer, HIV-1 Env, pre-fusion state Bartesaghi A Merk A Borgnia MJ Milne JLS Subramaniam S Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy NAT.STRUCT.MOL.BIOL. 20 1352 1357 2013 24154805 doi:10.1038/nsmb.2711 4cc8 FULLOVERLAP Complex of KNH1144 SOSIP gp140 trimer with VRC03 Fab. Complex of KNH1144 SOSIP gp140 trimer with VRC03 Fab. Tetramer (gp41, gp120, Fab Heavy, Fab Light) 4 0.67 gp120 Human immunodeficiency virus 1 HIV-1 isolate 00KE_KNH1144 HIV-1 3 monomer true Homo sapiens SOSIP-PPI4 and furin-pcDNA3.1 gp41 Human immunodeficiency virus 1 HIV-1 isolate 00KE_KNH1144 HIV-1
Complete ectodomain of HIV-1 Env from the Clade A strain KNH1144 inlcuding residues in the membrane proximal external region with the following residue substitutions A662E, S668N, and S676T
3 monomer true Homo sapiens SOSIP-PPI4 and furin-pcDNA3.1 Monoclonal antibody VRC03 Fab Heavy chain Homo sapiens 0.025
Fab fragment
true Homo sapiens HEK 293 Monoclonal antibody VRC03 Fab Light chain Homo sapiens 0.025
Fab fragment
true Homo sapiens HEK 293 singleParticle particle 0.65 7.5
TNE Buffer (10 mM Tris, 150 mM NaCl, 1 mM EDTA)
Protochips C-flat R 2/2, plasma cleaned
 ETHANE 100 FEI VITROBOT MARK IV blot for 6 seconds, blot offset of -2, plunge into an ethane slurry cooled by liquid nitrogen FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 80 1.5 2.5 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER 2011-08-09 GATAN ULTRASCAN 4000 (4k x 4k) 4713 10 16.
Particles were selected manually, classified in 2D using IMAGIC and 3D refinement was done with FREALIGN.
C3 6.0 FSC 0.143 CUT-OFF EMAN, IMAGIC, FREALIGN 88125 500 emd_2484.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 276.48 276.48 276.48 90.0 90.0 90.0 X Y Z -0.03569165 0.08147071 0.00132176 0.00755302 1.08 1.08 1.08 0.0405 AUTHOR Structure of HIV-1 gp140 trimer bound to VRC03 Fab
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 3SE8 G H L RIGID BODY FIT Chimera
3SE8, Chain G and chains H, L fitted as two separate rigid bodies into map. 3HMG helix fitted by hand into map.
REAL 3HMG B RIGID BODY FIT Chimera
Protocol: Rigid body. Automated fitting procedures. Only residues 92-122 of chain B were fitted.
REAL