5UKR

Structure of unliganded anti-gp120 CD4bs antibody DH522.2 Fab in complex with a gp120 core

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • 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; Duke University Center for AIDS Research 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.712 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 

wwPDB Validation  3D Report Full Report


This is version 1.0 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
  • Primary Citation of Related Structures:  5UKN, 5UKO, 5UKP, 5UKQ

  • 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 siteĀ (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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule Chains Sequence Length Organism Details
DH522.2 Fab fragment heavy chain
H
230 N/A N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
Molecule Chains Sequence Length Organism Details
DH522.2 Fab fragment light chain
L
216 N/A N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
Molecule Chains Sequence Length Organism Details
Chimeric B.YU2 gp120 core derived from HIV-1 Env
G
313 N/A N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.712 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å) Angle (°)
a = 50.851 α = 90.00
b = 71.973 β = 90.00
c = 252.228 γ = 90.00
Software Package:
Software Name Purpose
PHENIX refinement
HKL-2000 data reduction
PHASER phasing
HKL-2000 data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-23 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Nicely, N.I.

Funding Organization Country Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases United States UM1-AI100645
National Institutes of Health/National Institute Of Allergy and Infectious Diseases United States R01-AI087202
National Institutes of Health/National Institute Of Allergy and Infectious Diseases United States R01-AI118571
Duke University Center for AIDS Research United States P30-AI-64518

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release