7JKS | pdb_00007jks

Crystal structure of vaccine-elicited broadly neutralizing VRC01-class antibody 2411a in complex with HIV-1 gp120 core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 
    0.332 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.283 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 
    0.285 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Vaccination induces maturation in a mouse model of diverse unmutated VRC01-class precursors to HIV-neutralizing antibodies with >50% breadth.

Chen, X.Zhou, T.Schmidt, S.D.Duan, H.Cheng, C.Chuang, G.Y.Gu, Y.Louder, M.K.Lin, B.C.Shen, C.H.Sheng, Z.Zheng, M.X.Doria-Rose, N.A.Joyce, M.G.Shapiro, L.Tian, M.Alt, F.W.Kwong, P.D.Mascola, J.R.

(2021) Immunity 54: 324-339.e8

  • DOI: https://doi.org/10.1016/j.immuni.2020.12.014
  • Primary Citation of Related Structures:  
    7JKS, 7JKT

  • PubMed Abstract: 

    Vaccine elicitation of broadly neutralizing antibodies (bnAbs) is a key HIV-research goal. The VRC01 class of bnAbs targets the CD4-binding site on the HIV-envelope trimer and requires extensive somatic hypermutation (SHM) to neutralize effectively. Despite substantial progress, vaccine-induced VRC01-class antibodies starting from unmutated precursors have exhibited limited neutralization breadth, particularly against viruses bearing glycan on loop D residue N276 (glycan276), present on most circulating strains. Here, using sequential immunization of immunoglobulin (Ig)-humanized mice expressing diverse unmutated VRC01-class antibody precursors, we elicited serum responses capable of neutralizing viruses bearing glycan276 and isolated multiple lineages of VRC01-class bnAbs, including two with >50% breadth on a 208-strain panel. Crystal structures of representative bnAbs revealed the same mode of recognition as known VRC01-class bnAbs. Structure-function studies further pinpointed key mutations and correlated their induction with specific immunizations. VRC01-class bnAbs can thus be matured by sequential immunization from unmutated ancestors to >50% breadth, and we delineate immunogens and regimens inducing key SHM.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 gp120 coreA [auth G]375Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for H9DP89 (Human immunodeficiency virus type 1)
Explore H9DP89 
Go to UniProtKB:  H9DP89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9DP89
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
The heavy chain of antibody 2411aB [auth H]232Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
The light chain of antibody 2411aC [auth L]211Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free:  0.332 (Depositor), 0.330 (DCC) 
  • R-Value Work:  0.283 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 0.285 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.92α = 90
b = 188.33β = 90
c = 45.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary