5UKO | pdb_00005uko

Structure of unliganded anti-gp120 CD4bs antibody DH522IA Fab

• PDB DOI: https://doi.org/10.2210/pdb5UKO/pdb

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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

• PubMed: 29170366 
• DOI: https://doi.org/10.1038/s41467-017-01336-3
• Primary Citation Related Structures: 
  5UKN, 5UKO, 5UKP, 5UKQ, 5UKR


• 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 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.

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Organizational Affiliation: 
• Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
Boston University School of Medicine, Boston, MA, 02118, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA.
Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
Department of Immunology, Duke University, Durham, NC, 27710, USA.
Infectious Disease Research Institute, Seattle, WA, 98102, USA.
GSK Vaccines, Rixensart, 1330, Belgium.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. [e-mail].
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.27 kDa 
• Atom Count: 3,414 
• Modeled Residue Count: 437 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DH522IA Fab fragment heavy chain	A [auth H]	230	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH522IA Fab fragment light chain	B [auth L]	216	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.708	α = 90
b = 68.708	β = 90
c = 176.184	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1-AI100645
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI087202
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	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
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary