7RI2

Crystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site.

Zhou, T.Chen, L.Gorman, J.Wang, S.Kwon, Y.D.Lin, B.C.Louder, M.K.Rawi, R.Stancofski, E.D.Yang, Y.Zhang, B.Quigley, A.F.McCoy, L.E.Rutten, L.Verrips, T.Weiss, R.A.Doria-Rose, N.A.Shapiro, L.Kwong, P.D.

(2022) Structure 30: 862-875.e4

  • DOI: https://doi.org/10.1016/j.str.2022.03.012
  • Primary Citation of Related Structures:  
    7LPN, 7R73, 7R74, 7RI1, 7RI2

  • PubMed Abstract: 

    Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein 120382Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for C6G099 (Human immunodeficiency virus 1)
Explore C6G099 
Go to UniProtKB:  C6G099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6G099
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-HIV llama VHH antibody A12143Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.596α = 90
b = 66.596β = 90
c = 266.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary