9MJ3 | pdb_00009mj3

Crystal structure of the VRC01-class antibody 12A01, derived from GT1.1 vaccination, in complex with eOD-GT8

• PDB DOI: https://doi.org/10.2210/pdb9MJ3/pdb

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


• Deposited: 2024-12-13 Released: 2025-05-28 
• Deposition Author(s): Agrawal, S., Wilson, I.A.
• 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: 2.20 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: in silico

Literature

Precise targeting of HIV broadly neutralizing antibody precursors in humans.

Caniels, T.G., Prabhakaran, M., Ozorowski, G., MacPhee, K.J., Wu, W., van der Straten, K., Agrawal, S., Derking, R., Reiss, E.I.M.M., Millard, K., Turroja, M., Desrosiers, A., Bethony, J., Malkin, E., Liesdek, M.H., van der Veen, A., Klouwens, M., Snitselaar, J.L., Bouhuijs, J.H., Bronson, R., Jean-Baptiste, J., Gajjala, S., Rikhtegaran Tehrani, Z., Benner, A., Ramaswami, M., Duff, M.O., Liu, Y.W., Sato, A.H., Kim, J.Y., Baken, I.J.L., Mendes Silva, C., Bijl, T.P.L., van Rijswijk, J., Burger, J.A., Cupo, A., Yasmeen, A., Phulera, S., Lee, W.H., Randall Jr., K.N., Zhang, S., Corcoran, M.M., Regadas, I., Sullivan, A.C., Brown, D.M., Bohl, J.A., Greene, K.M., Gao, H., Yates, N.L., Sawant, S., Prins, J.M., Kootstra, N.A., Kaminsky, S.M., Barin, B., Rahaman, F., Meller, M., Philiponis, V., Laufer, D.S., Lombardo, A., Mwoga, L., Shotorbani, S., Holman, D., Koup, R.A., Klasse, P.J., Karlsson Hedestam, G.B., Tomaras, G.D., van Gils, M.J., Montefiori, D.C., McDermott, A.B., Hyrien, O., Moore, J.P., Wilson, I.A., Ward, A.B., Diemert, D.J., de Bree, G.J., Andrews, S.F., Caskey, M., Sanders, R.W.

(2025) Science 389: eadv5572-eadv5572

• PubMed: 40373114 
• DOI: https://doi.org/10.1126/science.adv5572
• Primary Citation Related Structures: 
  9MI0, 9MIA, 9MIB, 9MIC, 9MID, 9MIF, 9MIH, 9MII, 9MJ3, 9MJ6, 9MJC, 9MJD, 9MJI, 9MK4


• PubMed Abstract: 
  

  A protective HIV vaccine will need to induce broadly neutralizing antibodies (bnAbs) in humans, but priming rare bnAb precursor B cells has been challenging. In a double-blinded, placebo-controlled phase 1 human clinical trial, the recombinant, germline-targeting envelope glycoprotein (Env) trimer BG505 SOSIP.v4.1-GT1.1, adjuvanted with AS01 _B , induced bnAb precursors of the VRC01-class at a high frequency in the majority of vaccine recipients. These bnAb precursors, that target the CD4 receptor binding site, had undergone somatic hypermutation characteristic of the VRC01-class. A subset of isolated VRC01-class monoclonal antibodies neutralized wild-type pseudoviruses and was structurally extremely similar to bnAb VRC01. These results further support germline-targeting approaches for human HIV vaccine design and demonstrate atomic-level manipulation of B cell responses with rational vaccine design.

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Organizational Affiliation: 
• Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands.
Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
Vaccine Research Unit, The George Washington University, Washington, DC, USA.
Department of Internal Medicine, Amsterdam UMC, location AMC, Amsterdam, Netherlands.
Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Foundation for the National Institutes of Health, Inc., Bethesda, MD, USA.
Department of Surgery, Duke University Medical Center, Durham, NC, USA.
Department of Experimental Immunology, Amsterdam UMC, location AMC, Amsterdam, Netherlands.
Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
The Emmes Company, Rockville, MD, USA.
International AIDS Vaccine Initiative (IAVI), New York, NY, USA.
The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.64 kDa 
• Atom Count: 4,715 
• Modeled Residue Count: 592 
• Deposited Residue Count: 618 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12A01 Fab heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
12A01 Fab light chain	B [auth L]	209	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
eOD-GT8 engineered mutant of gp120	C	183	Human immunodeficiency virus 1	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.687	α = 90
b = 72.364	β = 90
c = 218.618	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
autoPROC	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Agrawal, S., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5P01AI110657

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release
  
• Version 1.1: 2025-06-04
  Changes: Database references
• Version 1.2: 2025-08-13
  Changes: Database references