Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs

REL RCSB RCSB RCSB 2013-10-26 2013-11-13 2013-11-13 2014-01-08 Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs Lyumkis D Julien JP de Val N Cupo A Potter CS Klasse PJ Burton DR Sanders RW Moore JP Carragher B Wilson IA Ward AB HIV-1 trimeric spike, gp140, SOSIP, broadly neutralizing antibody, PGV04, Env, Envelope glycoprotein Lyumkis D Julien JP de Val N Cupo A Potter CS Klasse PJ Burton DR Sanders RW Moore JP Carragher B Wilson IA Ward AB Cryo-EM Structure of a Fully Glycosylated Soluble Cleaved HIV-1 Envelope Trimer. SCIENCE 342 1484 1490 2013 24179160 doi:10.1126/science.1245627 3j5m FULLOVERLAP Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs three SOSIP.664 gp140 subunits (trimeric HIV-1 spike) with 3 PGV04 Fabs 2 0.6 BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140 Human immunodeficiency virus 1 BG505.W6M.ENV.A5 human immunodeficiency virus type I 0.6 3 trimer true Homo sapiens HEK 293T Fragment antigen binding Homo sapiens Human 0.05 0.05 3 heterodimer true Homo sapiens HEK 293F singleParticle particle 0.72 7.6

20 mM Tris, 150 mM NaCl, 0.085 mM DDM

400 mesh C-Flat CF-22-4C, plasma treated for 5 seconds

ETHANE HOMEMADE PLUNGER Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 seconds, followed by blotting with a small piece of filter paper and plunge-freezing into liquid ethane using a manual cryo-plunger in an ambient environment (4 degrees C). FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2 1.0 5.0 29000.0 29000.0 SIDE ENTRY, EUCENTRIC objective lens astigmatism was corrected by observing Thon rings with the Leginon software

electron counting mode

2013-02-21 GATAN K2 (4k x 4k) 5.0 6355 32

The dose was fractionated over 20 raw frames collected over a 5-second exposure time (250 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~9.4 e-/pixel/sec. The individual frames were aligned using a GPU-enabled frame-alignment program that was generously provided by Yifan Cheng and Xueming Li. This program was used to track the global shifts between individual frames.

Reconstructed using resolution-limited refinement procedure implemented in Xmipp and Frealign.

Frealign

OTHER 5.8 FSC 0.143 CUT-OFF Xmipp, Frealign

Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers.

49572 emd_5779.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.02848566 0.06708022 0.00017031 0.00453258 1.21 1.21 1.21 0.027 AUTHOR Cryo-EM structure of a fully glycosylated SOSIP.664 Env trimer with 3 broadly neutralizing PGV04 Fabs

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3SE9 REAL 2B4C REAL 3U2S REAL 1ENV REAL