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Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.354
f_angle_d
1.177
f_chiral_restr
0.06
f_bond_d
0.009
f_plane_restr
0.008
Sample
HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding
Sample Components
HIV-1 Env B41 SOSIP.664
CD4 (2-domain)
17b fragment antigen
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, follo ...
3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
46855
Reported Resolution (Å)
3.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C3
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
EMRinger
Overall B Value
Fitting Procedure
Details
Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. sCD4 and 17b coordinates taken from PDB 1GC1. Performed fragment based refine ...
Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. sCD4 and 17b coordinates taken from PDB 1GC1. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix.