8U1D | pdb_00008u1d

Cryo-EM structure of vaccine-elicited CD4 binding site antibody DH1285 bound to HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env Local Refinement

• PDB DOI: https://doi.org/10.2210/pdb8U1D/pdb
• EM Map EMD-41810: EMDB EMDataResource

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


• Deposited: 2023-08-31 Released: 2024-01-03 
• Deposition Author(s): Thakur, B., Stalls, V.D., Acharya, P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Vaccine induction of CD4-mimicking HIV-1 broadly neutralizing antibody precursors in macaques.

Saunders, K.O., Counts, J., Thakur, B., Stalls, V., Edwards, R., Manne, K., Lu, X., Mansouri, K., Chen, Y., Parks, R., Barr, M., Sutherland, L., Bal, J., Havill, N., Chen, H., Machiele, E., Jamieson, N., Hora, B., Kopp, M., Janowska, K., Anasti, K., Jiang, C., Van Itallie, E., Venkatayogi, S., Eaton, A., Henderson, R., Barbosa, C., Alam, S.M., Santra, S., Weissman, D., Moody, M.A., Cain, D.W., Tam, Y.K., Lewis, M., Williams, W.B., Wiehe, K., Montefiori, D.C., Acharya, P., Haynes, B.F.

(2024) Cell 187: 79-94.e24

• PubMed: 38181743 
• DOI: https://doi.org/10.1016/j.cell.2023.12.002
• Primary Citation Related Structures: 
  8U1D


• PubMed Abstract: 
  

  The CD4-binding site (CD4bs) is a conserved epitope on HIV-1 envelope (Env) that can be targeted by protective broadly neutralizing antibodies (bnAbs). HIV-1 vaccines have not elicited CD4bs bnAbs for many reasons, including the occlusion of CD4bs by glycans, expansion of appropriate naive B cells with immunogens, and selection of functional antibody mutations. Here, we demonstrate that immunization of macaques with a CD4bs-targeting immunogen elicits neutralizing bnAb precursors with structural and genetic features of CD4-mimicking bnAbs. Structures of the CD4bs nAb bound to HIV-1 Env demonstrated binding angles and heavy-chain interactions characteristic of all known human CD4-mimicking bnAbs. Macaque nAb were derived from variable and joining gene segments orthologous to the genes of human VH1-46-class bnAb. This vaccine study initiated in primates the B cells from which CD4bs bnAbs can derive, accomplishing the key first step in the development of an effective HIV-1 vaccine.

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Organizational Affiliation: 
• Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: [e-mail].
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.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA.
Acuitas LLC, Vancouver, BC, Canada.
Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.
BIOQUAL, Rockville, MD 20850, USA.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: [e-mail].
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: [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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 124.53 kDa 
• Atom Count: 5,109 
• Modeled Residue Count: 650 
• Deposited Residue Count: 1,123 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A	647	Human immunodeficiency virus 1	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1285 Heavy Chain	B [auth I]	243	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1285 Light Chain	C [auth J]	233	Macaca mulatta	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): Thakur, B., Stalls, V.D., Acharya, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI145687
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144371

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release
  
• Version 1.1: 2024-07-17
  Changes: Data collection, Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.3: 2025-06-04
  Changes: Data collection