4RFO

Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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This is version 1.5 of the entry. See complete history


Literature

Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.

Gohain, N.Tolbert, W.D.Acharya, P.Yu, L.Liu, T.Zhao, P.Orlandi, C.Visciano, M.L.Kamin-Lewis, R.Sajadi, M.M.Martin, L.Robinson, J.E.Kwong, P.D.DeVico, A.L.Ray, K.Lewis, G.K.Pazgier, M.

(2015) J Virol 89: 8840-8854

  • DOI: https://doi.org/10.1128/JVI.01232-15
  • Primary Citation of Related Structures:  
    4RFE, 4RFN, 4RFO

  • PubMed Abstract: 

    Accumulating evidence indicates a role for Fc receptor (FcR)-mediated effector functions of antibodies, including antibody-dependent cell-mediated cytotoxicity (ADCC), in prevention of human immunodeficiency virus type 1 (HIV-1) acquisition and in postinfection control of viremia. Consequently, an understanding of the molecular basis for Env epitopes that constitute effective ADCC targets is of fundamental interest for humoral anti-HIV-1 immunity and for HIV-1 vaccine design. A substantial portion of FcR effector function of potentially protective anti-HIV-1 antibodies is directed toward nonneutralizing, transitional, CD4-inducible (CD4i) epitopes associated with the gp41-reactive region of gp120 (cluster A epitopes). Our previous studies defined the A32-like epitope within the cluster A region and mapped it to the highly conserved and mobile layers 1 and 2 of the gp120 inner domain within the C1-C2 regions of gp120. Here, we elucidate additional cluster A epitope structures, including an A32-like epitope, recognized by human monoclonal antibody (MAb) N60-i3, and a hybrid A32-C11-like epitope, recognized by rhesus macaque MAb JR4. These studies define for the first time a hybrid A32-C11-like epitope and map it to elements of both the A32-like subregion and the seven-layered β-sheet of the gp41-interactive region of gp120. These studies provide additional evidence that effective antibody-dependent effector function in the cluster A region depends on precise epitope targeting--a combination of epitope footprint and mode of antibody attachment. All together these findings help further an understanding of how cluster A epitopes are targeted by humoral responses.


  • Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 clade A/E gp120A [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: HIV-1 env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED31
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
m48u1 CD4 mimetic peptideB [auth N]28synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N60-i3 Fab heavy chainC [auth H]229Homo sapiensMutation(s): 0 
Gene Names: FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-i3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
N60-i3 Fab light chainD [auth L]221Homo sapiensMutation(s): 0 
Gene Names: FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-i3
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.305α = 90
b = 102.575β = 90
c = 108.038γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-06-02
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2023-12-06
    Changes: Data collection