9D8Y image
Deposition Date 2024-08-20
Release Date 2025-04-30
Last Version Date 2025-10-01
Entry Detail
PDB ID:
9D8Y
Title:
Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated, Population 4
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.06 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Envelope glycoprotein gp160
Mutagens:T332N, A501C
Chain IDs:A, B, C
Chain Length:469
Number of Molecules:3
Biological Source:Human immunodeficiency virus 1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Envelope glycoprotein gp160
Gene (Uniprot):env
Mutagens:I559P,T605C
Chain IDs:D, E, F
Chain Length:153
Number of Molecules:3
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Molecule:VRC34.01 Fab Heavy Chain
Chain IDs:G, I, K
Chain Length:223
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:VRC34.01 Fab Light Chain
Chain IDs:H, J, L
Chain Length:212
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:T-cell surface glycoprotein CD4
Gene (Uniprot):CD4
Chain IDs:M, N, O
Chain Length:96
Number of Molecules:3
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening.
Nat Commun 16 4595 4595 (2025)
PMID: 40382314 DOI: 10.1038/s41467-025-59721-2

Abstact

The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminus of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41. The gp120/gp41 heterodimer assembles into a homotrimer, in which FP is accessible for antibody binding. Env conformational changes or "opening" that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibodies. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains, we visualize that the FP remains accessible for antibody binding despite substantial receptor-induced Env opening. We delineate stepwise Env opening from its closed state to a functional CD4-bound symmetrically open Env in which we show that FP was accessible for antibody binding. We define downstream re-organizations that lead to the formation of a gp120/gp41 cavity into which the FP buries to become inaccessible for antibody binding. These findings improve our understanding of HIV-1 entry and delineate the entry-related conformational trajectory of a key site of HIV vulnerability to neutralizing antibody.

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Primary Citation of related structures
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