9MPB | pdb_00009mpb

Crystal structure of the HIV V2-apex-targeting antibody RM038, derived from macaque ApexGT6 immunization

• PDB DOI: https://doi.org/10.2210/pdb9MPB/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-30 Released: 2025-07-30 
• Deposition Author(s): Agrawal, S., Wilson, I.A.
• Funding Organization(s): International AIDS Vaccine Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: in silico

Literature

HIV broadly neutralizing antibody precursors to the Apex epitope induced in nonhuman primates.

Ma, K.M., Sutton, H.J., Pratap, P.P., Steichen, J.M., Carnathan, D., Quinn, J., Kalyuzhniy, O., Liguori, A., Agrawal, S., Baboo, S., Madden, P., Cottrell, C.A., Willis, J.R., Lee, J.H., Landais, E., Hu, X., Ramezani-Rad, P., Ozorowski, G., Lewis, V.R., Diedrich, J.K., Zhou, X., Altheide, T.K., Phelps, N., Georgeson, E., Alavi, N.B., Lu, D., Eskandarzadeh, S., Kubitz, M., Adachi, Y., Mullen, T.M., Silva, M., Melo, M.B., Himansu, S., Irvine, D.J., Burton, D.R., Yates 3rd, J.R., Paulson, J.C., Sok, D., Wilson, I.A., Silvestri, G., Ward, A.B., Crotty, S., Schief, W.R.

(2025) Sci Immunol 10: eadt6660-eadt6660

• PubMed: 40845127 
• DOI: https://doi.org/10.1126/sciimmunol.adt6660
• Primary Citation of Related Structures:  
  9B8B, 9B8C, 9MPB, 9MPC, 9MQG


• PubMed Abstract: 
  

  An effective prophylactic HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). bnAbs to the Apex region of the HIV envelope glycoprotein (Env) are promising targets for vaccination because of their relatively low somatic hypermutation compared with other bnAbs. Most Apex bnAbs engage Env using an exceptionally long heavy-chain complementarity-determining region 3 (HCDR3) containing specific binding motifs, which reduces bnAb precursor frequency and makes priming of rare bnAb precursors a likely limiting step in the path to Apex bnAb induction. We found that adjuvanted protein or mRNA lipid nanoparticle (LNP) immunization of rhesus macaques with ApexGT6, an Env trimer engineered to bind Apex bnAb precursors, consistently induced Apex bnAb-related precursors with long HCDR3s bearing bnAb-like sequence motifs. Cryo-electron microscopy revealed that elicited Apex bnAb-related HCDR3s had structures combining elements of several prototype Apex bnAbs. These results achieve a critical HIV vaccine development milestone in outbred primates.

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Organizational Affiliation: 
• Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA.
IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA.
Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA.
Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Moderna Inc., Cambridge, MA 02139, USA.
David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.
Department of Materials Science and Engineering, MIT, Cambridge, MA 02139, USA.
Department of Biological Engineering, MIT, Cambridge, MA 02139, USA.
Ragon Institute of Massachusetts General Hospital, Cambridge, MA 02139, USA.
Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037 USA.

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: 49.43 kDa 
• Atom Count: 3,549 
• Modeled Residue Count: 444 
• Deposited Residue Count: 457 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H]	237	Macaca	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	B [auth L]	220	Macaca	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	A [auth H]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.251	α = 90
b = 66.512	β = 103.18
c = 53.405	γ = 90

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: 2025-07-30 
Deposition Author(s): Agrawal, S., Wilson, I.A.

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Funding Organization	Location	Grant Number
International AIDS Vaccine Initiative	United States	INV-034657
International AIDS Vaccine Initiative	United States	INV-064772

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Database references