6XCJ | pdb_00006xcj

Crystal Structure of DH650 Fab from a Rhesus Macaque in Complex with HIV-1 gp120 Core

• PDB DOI: https://doi.org/10.2210/pdb6XCJ/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Macaca mulatta
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-08 Released: 2020-12-02 
• Deposition Author(s): Raymond, D.D., Chug, H., Harrison, S.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.284 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth.

Roark, R.S., Li, H., Williams, W.B., Chug, H., Mason, R.D., Gorman, J., Wang, S., Lee, F.H., Rando, J., Bonsignori, M., Hwang, K.K., Saunders, K.O., Wiehe, K., Moody, M.A., Hraber, P.T., Wagh, K., Giorgi, E.E., Russell, R.M., Bibollet-Ruche, F., Liu, W., Connell, J., Smith, A.G., DeVoto, J., Murphy, A.I., Smith, J., Ding, W., Zhao, C., Chohan, N., Okumura, M., Rosario, C., Ding, Y., Lindemuth, E., Bauer, A.M., Bar, K.J., Ambrozak, D., Chao, C.W., Chuang, G.Y., Geng, H., Lin, B.C., Louder, M.K., Nguyen, R., Zhang, B., Lewis, M.G., Raymond, D.D., Doria-Rose, N.A., Schramm, C.A., Douek, D.C., Roederer, M., Kepler, T.B., Kelsoe, G., Mascola, J.R., Kwong, P.D., Korber, B.T., Harrison, S.C., Haynes, B.F., Hahn, B.H., Shaw, G.M.

(2021) Science 371

• PubMed: 33214287 
• DOI: https://doi.org/10.1126/science.abd2638
• Primary Citation Related Structures: 
  6XCJ, 6XRT


• PubMed Abstract: 
  

  Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.

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Organizational Affiliation: 
• Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Departments of Immunology and Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
Departments of Pediatrics and Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Bioqual, Inc., Rockville, MD 20850, USA.
Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA.
Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA.
Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 90.13 kDa 
• Atom Count: 5,712 
• Modeled Residue Count: 721 
• Deposited Residue Count: 803 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope Glycoprotein gp120	A [auth G]	357	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for A0A0A7I3C6 (Human immunodeficiency virus type 1) Explore A0A0A7I3C6  Go to UniProtKB:  A0A0A7I3C6
Glycosylation
Glycosylation Sites: 9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH650 Fab Heavy Chain	B [auth H]	226	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH650 Fab Light Chain	C [auth L]	220	Macaca mulatta	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.284 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.52	α = 90
b = 122.1	β = 90
c = 53.4	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Raymond, D.D., Chug, H., Harrison, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI144371

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2021-01-20
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary