5WDF

Crystal structure of 10E8v4-5R+100cF Fab in complex with HIV-1 gp41 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Surface-Matrix Screening Identifies Semi-specific Interactions that Improve Potency of a Near Pan-reactive HIV-1-Neutralizing Antibody.

Kwon, Y.D.Chuang, G.Y.Zhang, B.Bailer, R.T.Doria-Rose, N.A.Gindin, T.S.Lin, B.Louder, M.K.McKee, K.O'Dell, S.Pegu, A.Schmidt, S.D.Asokan, M.Chen, X.Choe, M.Georgiev, I.S.Jin, V.Pancera, M.Rawi, R.Wang, K.Chaudhuri, R.Kueltzo, L.A.Manceva, S.D.Todd, J.P.Scorpio, D.G.Kim, M.Reinherz, E.L.Wagh, K.Korber, B.M.Connors, M.Shapiro, L.Mascola, J.R.Kwong, P.D.

(2018) Cell Rep 22: 1798-1809

  • DOI: https://doi.org/10.1016/j.celrep.2018.01.023
  • Primary Citation of Related Structures:  
    5WDF

  • PubMed Abstract: 

    Highly effective HIV-1-neutralizing antibodies could have utility in the prevention or treatment of HIV-1 infection. To improve the potency of 10E8, an antibody capable of near pan-HIV-1 neutralization, we engineered 10E8-surface mutants and screened for improved neutralization. Variants with the largest functional enhancements involved the addition of hydrophobic or positively charged residues, which were positioned to interact with viral membrane lipids or viral glycan-sialic acids, respectively. In both cases, the site of improvement was spatially separated from the region of antibody mediating molecular contact with the protein component of the antigen, thereby improving peripheral semi-specific interactions while maintaining unmodified dominant contacts responsible for broad recognition. The optimized 10E8 antibody, with mutations to phenylalanine and arginine, retained the extraordinary breadth of 10E8 but with ∼10-fold increased potency. We propose surface-matrix screening as a general method to improve antibodies, with improved semi-specific interactions between antibody and antigen enabling increased potency without compromising breadth.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
10E8v4-5R+100cF Fab heavy chainA [auth H],
C [auth A]
232Homo sapiensMutation(s): 0 
Gene Names: 1GHG1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FA10E8v4-5R+100cF FAB light chainB [auth L],
D [auth B]
214Homo sapiensMutation(s): 0 
Gene Names: IGLC2
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 gp41 peptideE [auth P],
F [auth Q]
17Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
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UniProt GroupP04578
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.284α = 103.08
b = 60.953β = 107.46
c = 70.149γ = 100.05
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description