6W4M

CRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV CO-RECEPTOR BINDING SITE ANTIBODY N12-I2 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: 0.301 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site.

Tolbert, W.D.Sherburn, R.Gohain, N.Ding, S.Flinko, R.Orlandi, C.Ray, K.Finzi, A.Lewis, G.K.Pazgier, M.

(2020) BMC Biol 18: 91-91

  • DOI: https://doi.org/10.1186/s12915-020-00819-y
  • Primary Citation of Related Structures:  
    6W4M

  • PubMed Abstract: 

    The binding of HIV-1 Envelope glycoproteins (Env) to host receptor CD4 exposes vulnerable conserved epitopes within the co-receptor binding site (CoRBS) which are required for the engagement of either CCR5 or CXCR4 co-receptor to allow HIV-1 entry. Antibodies against this region have been implicated in the protection against HIV acquisition in non-human primate (NHP) challenge studies and found to act synergistically with antibodies of other specificities to deliver effective Fc-mediated effector function against HIV-1-infected cells. Here, we describe the structure and function of N12-i2, an antibody isolated from an HIV-1-infected individual, and show how the unique structural features of this antibody allow for its effective Env recognition and Fc-mediated effector function.


  • Organizational Affiliation

    Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
clade A/E 93TH057 HIV-1 gp120 coreA [auth G]353Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1)
Explore A0A0M3KKW9 
Go to UniProtKB:  A0A0M3KKW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKW9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAINB [auth L]215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAINC [auth H]239Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
M48U1 CD4 MIMETIC PEPTIDED [auth N]28synthetic constructMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.687α = 90
b = 69.522β = 90
c = 213.468γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI116274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI129769
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI120756

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection