5UKN

Structure of unliganded anti-gp120 CD4bs antibody DH522UCA Fab

  • Classification: IMMUNE SYSTEM
  • Organism(s): Macaca mulatta
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2017-01-23 Released: 2017-12-06 
  • Deposition Author(s): Nicely, N.I.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Duke University Center for AIDS Research

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations.

Williams, W.B., Zhang, J., Jiang, C., Nicely, N.I., Fera, D., Luo, K., Moody, M.A., Liao, H.X., Alam, S.M., Kepler, T.B., Ramesh, A., Wiehe, K., Holland, J.A., Bradley, T., Vandergrift, N., Saunders, K.O., Parks, R., Foulger, A., Xia, S.M., Bonsignori, M., Montefiori, D.C., Louder, M., Eaton, A., Santra, S., Scearce, R., Sutherland, L., Newman, A., Bouton-Verville, H., Bowman, C., Bomze, H., Gao, F., Marshall, D.J., Whitesides, J.F., Nie, X., Kelsoe, G., Reed, S.G., Fox, C.B., Clary, K., Koutsoukos, M., Franco, D., Mascola, J.R., Harrison, S.C., Haynes, B.F., Verkoczy, L.

(2017) Nat Commun 8: 1732-1732

  • DOI: 10.1038/s41467-017-01336-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • A strategy for HIV-1 vaccine development is to define envelope (Env) evolution of broadly neutralizing antibodies (bnAbs) in infection and to recreate those events by vaccination. Here, we report host tolerance mechanisms that limit the development o ...

    A strategy for HIV-1 vaccine development is to define envelope (Env) evolution of broadly neutralizing antibodies (bnAbs) in infection and to recreate those events by vaccination. Here, we report host tolerance mechanisms that limit the development of CD4-binding site (CD4bs), HCDR3-binder bnAbs via sequential HIV-1 Env vaccination. Vaccine-induced macaque CD4bs antibodies neutralize 7% of HIV-1 strains, recognize open Env trimers, and accumulate relatively modest somatic mutations. In naive CD4bs, unmutated common ancestor knock-in mice Env + B cell clones develop anergy and partial deletion at the transitional to mature B cell stage, but become Env - upon receptor editing. In comparison with repetitive Env immunizations, sequential Env administration rescue anergic Env + (non-edited) precursor B cells. Thus, stepwise immunization initiates CD4bs-bnAb responses, but immune tolerance mechanisms restrict their development, suggesting that sequential immunogen-based vaccine regimens will likely need to incorporate strategies to expand bnAb precursor pools.

    Organizational Affiliation: 

    Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. Laurent.verkoczy@dm.duke.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DH522UCA Fab fragment heavy chainH230Macaca mulattaMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH522UCA Fab fragment light chainL216Macaca mulattaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.524α = 90
b = 68.524β = 90
c = 178.381γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-23 
  • Released Date: 2017-12-06 
    • Deposition Author(s): Nicely, N.I.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1-AI100645
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI087202
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI118571
Duke University Center for AIDS ResearchUnited StatesP30-AI-64518

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence