Extended Data Fig. 2. Data processing for BG505 SOSIP-sCD4-E51 complex structures.

a, Example of a motion-corrected and dose-weighted micrograph of E51-sCD4-BG505 complexes (representative individual particles in boxes). Scale bar = 50 nm. Defocus was ~2.6 μm underfocus. b, Data processing scheme. Collected micrographs were motion-corrected using MotionCor2 (ref.¹) without binning. Contrast transfer functions (CTFs) were estimated using Gctf 1.06 (ref.²). ~1,000 particles were manually picked and subjected to 2D classification in RELION^3,4. Particles from good classes were used as references for automatic particle picking using RELION AutoPicking. 941,841 autopicked particles were subjected to three rounds of reference-free 2D classification. In each round, particles from good 2D classes were selected, which gave 656,059 particles. Subsequently, using the Env trimer portion of an 80 Å low-pass filtered partially-open trimeric BG505 SOSIP structure (PDB 6CM3) as the reference model, first round of 3D classification was performed assuming C1 symmetry. Particles from good classes were combined and used for a second round of 3D classification with C1 symmetry. The resulting maps could be grouped into two classes: class I (320,895 particles) and class II (182,970 particles). Maps from the two classes were refined separately assuming C1 symmetry with the sCD4 D2 domain and E51 Fab C_HC_L domains masked out. After CTF refinement, movie refinement, and particle polishing, the class I and class II post-processed maps were refined to 3.3 Å and 3.5 Å resolution (FSC 0.143), respectively (Fig. S3).