8D01 | pdb_00008d01

The domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13

• PDB DOI: https://doi.org/10.2210/pdb8D01/pdb

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


• Deposited: 2022-05-25 Released: 2023-12-13 
• Deposition Author(s): Xian, Y., Wilson, I.A.
• Funding Organization(s): International AIDS Vaccine Initiative, Consortia for HIV/AIDS Vaccine Development, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site.

Caniels, T.G., Medina-Ramirez, M., Zhang, S., Kratochvil, S., Xian, Y., Koo, J.H., Derking, R., Samsel, J., van Schooten, J., Pecetta, S., Lamperti, E., Yuan, M., Carrasco, M.R., Del Moral Sanchez, I., Allen, J.D., Bouhuijs, J.H., Yasmeen, A., Ketas, T.J., Snitselaar, J.L., Bijl, T.P.L., Martin, I.C., Torres, J.L., Cupo, A., Shirreff, L., Rogers, K., Mason, R.D., Roederer, M., Greene, K.M., Gao, H., Silva, C.M., Baken, I.J.L., Tian, M., Alt, F.W., Pulendran, B., Seaman, M.S., Crispin, M., van Gils, M.J., Montefiori, D.C., McDermott, A.B., Villinger, F.J., Koup, R.A., Moore, J.P., Klasse, P.J., Ozorowski, G., Batista, F.D., Wilson, I.A., Ward, A.B., Sanders, R.W.

(2024) Sci Immunol 9: eadk9550-eadk9550

• PubMed: 39213338 
• DOI: https://doi.org/10.1126/sciimmunol.adk9550
• Primary Citation of Related Structures:  
  8D01, 8SW3, 8SW4


• PubMed Abstract: 
  

  Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.

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Organizational Affiliation: 
• Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands.
Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands.
Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.
Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA.
Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA.
Institute for Biomedical Sciences, George Washington University, Washington, DC, USA.
School of Biological Sciences, University of Southampton, Southampton, UK.
Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA.
Duke University Medical Center, Durham, NC, USA.
Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 95.56 kDa 
• Atom Count: 6,980 
• Modeled Residue Count: 855 
• Deposited Residue Count: 876 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
21N13 Fab heavy chain	A [auth H], C [auth A]	225	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
21N13 Fab light chain	B [auth L], D [auth B]	213	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 260.367	α = 90
b = 45.151	β = 98.609
c = 84.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Xian, Y., Wilson, I.A.

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Funding Organization	Location	Grant Number
International AIDS Vaccine Initiative	United States	INV-008352/OPP1153692
Consortia for HIV/AIDS Vaccine Development	United States	CHAVD 1UM1 AI144462
Other private		P01 AI110657

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-30
  Changes: Structure summary
• Version 1.3: 2025-07-02
  Changes: Database references