6UBI

N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage.

Shen, C.H.DeKosky, B.J.Guo, Y.Xu, K.Gu, Y.Kilam, D.Ko, S.H.Kong, R.Liu, K.Louder, M.K.Ou, L.Zhang, B.Chao, C.W.Corcoran, M.M.Feng, E.Huang, J.Normandin, E.O'Dell, S.Ransier, A.Rawi, R.Sastry, M.Schmidt, S.D.Wang, S.Wang, Y.Chuang, G.Y.Doria-Rose, N.A.Lin, B.Zhou, T.Boritz, E.A.Connors, M.Douek, D.C.Karlsson Hedestam, G.B.Sheng, Z.Shapiro, L.Mascola, J.R.Kwong, P.D.

(2020) Cell Host Microbe 27: 531

  • DOI: 10.1016/j.chom.2020.01.027
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutraliz ...

    Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutralizing and non-broadly neutralizing branches of an antibody-developmental tree. Because sequences of antibodies isolated from the fusion peptide (FP)-targeting VRC34-antibody lineage suggested it might be suitable for such rare mutation analysis, we carried out next-generation sequencing (NGS) on B cell transcripts from donor N123, the source of the VRC34 lineage, and functionally and structurally characterized inferred intermediates along broadly neutralizing and poorly neutralizing developmental branches. The broadly neutralizing VRC34.01 branch required the rare heavy-chain mutation Y33P to bind FP, whereas the early bifurcated VRC34.05 branch did not require this rare mutation and evolved less breadth. Our results demonstrate how a required rare mutation can restrict development and shape the maturation of a broad HIV-1-neutralizing antibody lineage.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Electronic address: pdkwong@nih.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VRC34.05 heavy chainA, D229Homo sapiensMutation(s): 0 
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VRC34.05 light chainB, E212Homo sapiensMutation(s): 0 
Find proteins for Q6GMX0 (Homo sapiens)
Explore Q6GMX0 
Go to UniProtKB:  Q6GMX0
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV fusion peptide 512-519C, F8Human immunodeficiency virus 1Mutation(s): 0 
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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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.933α = 90
b = 44.278β = 96.2
c = 125.375γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references