Extended Data Table 1.

Cryo-EM data collection, refinement and validation statistics.

	CD4-gp120-CCR5 complex masked (EMDB -9108) (PDB 6MEO)	CD4-gp120-CCR5 complex overall (EMDB -9109) (PDB 6MET)
Data collection and processing
Magnification	130000	130000
Voltage (kV)	300	300
Electron exposure (e—/A2)	—46	—46
Defocus range (pa)	1-2.8	1-2.8
Pixel size (A)	0.529	0.529
Symmetry imposed	Cl	Cl
Initial particle images (no.)	1,707,575	1,707,575
Final particle images (no.)	307346	307346
Map resolution (A)	3.9	4.5
FSC threshold	0.143	0.143
Refinement
Initial model used (PDB code)	5UIW, 1WIO, 2QAD and 5VN3	5UIW, 1WIO, 2QAD and 5VN3
Map sharpening B factor (A2)	−190	−190
Model composition
Non-hydrogen atoms	7462	8911
Protein residues	887	1074
Ligands	32	32
R.m.s. deviations
Bond lengths (A)	0.004	0.009
Bond angles (°)	0.954	1.386
Validation
MolProbity score	1.60	1.97
Clashscore	3.51	5.84
Poor rotamers (%)	0.25	1.48
Ramachandran plot
Favored (%)	92.77	90.83
Allowed (%)	7.23	8.51
Disallowed (%)	0	0.66