REL RCSB RCSB RCSB 2013-03-27 2013-04-10 2013-07-03 2013-07-03 Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans Khayat R Lee JH Julien JP Wilson IA Ward AB Single particle analysis, uranyl formate, tilt series, antibody, HIV gp120 trimer, Fab Julien JP Sok D Khayat R Lee JH Doores KJ Walker LM Ramos A Diwanji DC Pejchal R Cupo A Katpally U Depetris RS Stanfield RL McBride R Marozsan AJ Paulson JC Sanders RW Moore JP Burton DR Poignard P Ward AB Wilson IA Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. PLOS PATHOG. 9 e1003342 e1003342 2013 23658524 doi:10.1371/journal.ppat.1003342 Fab fragment of broadly neutralizing antibody PGT122 in complex with HIV-1 SOSIP.664 from BG505 Fab fragment of broadly neutralizing antibody PGT122 in complex with HIV-1 SOSIP.664 from BG505
The sample was monodisperse
one SOSIP.664 trimer binds 3 PGT122 Fabs 2 0.35 0.35 SDS-PAGE BG505 HIV-1 Env SOSIP.664 Human immunodeficiency virus 1 BG505 HIV-1 0.22 0.22
Bound to Fab portion of PGT122 antibody
3 Trimer true Homo sapiens HEK 293S GnT I-deficient cells singleParticle particle 0.1 7.0
20 mM Tris-HCl, pH 7.0, 50 mM NaCl
 NEGATIVE
Grids were briefly adsorbed with protein, wicked, and stained with 2% Nano-W for 30 seconds.
400 Cu mesh grid with thin carob support, glow discharged in natural atmosphere.
 NONE OTHER FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 120 0.6 0.72 100000.0 100000.0 SIDE ENTRY, EUCENTRIC 293 294 293 Astigmatism of objective lens was corrected at 100,000x -2 2012-04-30 GENERIC GATAN (4k x 4k) 0.109 340 16 0 55
All particles were automatically selected from micrographs with DoG Picker [63]. Contrast Transfer function (CTF) estimation for the untilted and tilted micrographs was determined with ctffind3 and ctftilt [64]. Particles were binned by 4 (80x80 sized boxes) and reference-free 2D class averages were calculated using the Sparx package (Fig. S4) [65]. Forty ab initio models were generated from the final reference-free 2D class averages using the EMAN2 package. Each model was then refined against the reference-free 2D class averages using Sparx [65,66]. The model exhibiting Fab-like density was used as the initial model for iterative image reconstruction against the CTF-corrected particles using Sparx [65].
each image
 OTHER 14.0 FSC 0.5 CUT-OFF Sparx
Final map was calculated from a single data set. Multiple data sets produced indistinguishable maps, but data were not combined.
10413
SPIDER: theta 45 degrees, phi 45 degrees
 64 emd_5624.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 348.80002 348.80002 348.80002 90.0 90.0 90.0 X Y Z -1.24171531 12.395413400000001 0.0 0.99999994 2.18 2.18 2.18 3.87 AUTHOR Reconstruction of SOSIP.664 HIV-1 envelope trimer in complex with broadly neutralizing PGT122 Fab
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