3J5M

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

ELECTRON MICROSCOPY

Sample
Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 Fabs
Sample Components
BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp140
Fragment antigen binding

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	3 uL sample applied to grid, adsorbed for 30 seconds, blotted, and plunge-frozen in liquid ethane

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	49572
Reported Resolution (Å)	5.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers (Single particle details: reconstructed using a re ...	Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers (Single particle details: reconstructed using a resolution-limited refinement procedure implemented in Xmipp and Frealign) (Single particle--Applied symmetry: C3)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (3SE9, 2B4C, 3U2S, 1ENV)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	32

Imaging Experiment	1
Date of Experiment	2013-02-21
Temperature (Kelvin)
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	5000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	SIDE ENTRY, EUCENTRIC
Nominal Magnification	29000
Calibrated Magnification	29000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	electron counting mode

EM Software
Task	Software Package	Version
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	Xmipp

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Frealign

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.