9YIL | pdb_00009yil

HIV-1 Env del8-3fill SOSIP

• PDB DOI: https://doi.org/10.2210/pdb9YIL/pdb
• EM Map EMD-72994: EMDB EMDataResource

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


• Deposited: 2025-10-01 Released: 2026-05-27 
• Deposition Author(s): Gavor, E., Gristick, H.B., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Induction of broadly neutralizing HIV antibodies by a two-step mechanism informs vaccine design.

Skelly, A.N., Gristick, H.B., Li, H., Gavor, E., Connell, A.J., Kreider, E.F., Marchitto, L., Hogarty, M.P., Newby, M.L., Allen, J.D., Liu, W., West Jr., A.P., Ayyanathan, K., Campion, M.S., Winters, K., Gordon, C.G., Osbaldeston, R.A., Akeley, M.J., Lewis, E., Li, Y., Singh, A., Cruickshank, K., Park, Y., Zhao, C., Li, X., Amereh, K., Van Itallie, E., Carey, J.W., Albertus, A., DeLaitsch, A.T., Keeffe, J.R., Lituchy, M.G., Walsh, A.A., Morris, D.J., Habib, R., Bibollet-Ruche, F., Mishra, N., Avillion, G., Koranda, N.S., Plante, S.J., Martella, C.L., Lora, J., Wang, E.J.D., Lewis, M.G., Martin, M.A., Nussenzweig, M.C., Seaman, M.S., Irvine, D.J., Wiehe, K.J., Haynes, B.F., Wagh, K., Korber, B., Andrabi, R., Crispin, M., Weissman, D., Bjorkman, P.J., Hahn, B.H., Shaw, G.M.

(2026) Science : eaec6396-eaec6396

• PubMed: 42096521 
• DOI: https://doi.org/10.1126/science.aec6396
• Primary Citation Related Structures: 
  9YHO, 9YHQ, 9YHR, 9YHT, 9YIB, 9YID, 9YIE, 9YIF, 9YIG, 9YIH, 9YII, 9YIJ, 9YIK, 9YIL


• PubMed Abstract: 
  

  A major obstacle confronting HIV-1 vaccine and cure research is the lack of an outbred animal model for rapid and consistent induction of broadly neutralizing antibodies (bNAbs). We designed an epitope-focused simian-human immunodeficiency virus (SHIV.5MUT) that elicited broad and potent V3-glycan-targeted antibodies within a year of infection in 14 of 22 macaques compared with 0 of 14 control animals. SHIV.5MUT elicited bNAbs by a two-step mechanism, inducing an initial wave of V1-directed antibodies that selected for Envs with shortened, hypoglycosylated V1 loops, which in turn primed V3-glycan bNAb precursors. Rhesus bNAbs were immunogenetically and structurally diverse, closely resembling human V3-glycan bNAbs. Env-bNAb coevolution revealed a diverse repertoire of bNAb precursors and the Env variants that matured them, yielding a molecular blueprint for vaccine design.

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Organizational Affiliation: 
• Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
School of Biological Sciences, University of Southampton, Southampton, UK.
Duke Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA.
Bioqual, Inc., Rockville, MD, USA.
Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA.
Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Los Alamos National Laboratory, Los Alamos, NM, USA.
New Mexico Consortium, Los Alamos, NM, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 224.44 kDa 
• Atom Count: 13,917 
• Modeled Residue Count: 1,647 
• Deposited Residue Count: 1,872 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	A [auth C], C [auth B], E [auth A]	153	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B [auth G], D [auth F], F [auth E]	471	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6
Glycosylation
Glycosylation Sites: 14

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D], I, J, K, L, N, O, P, Q, S, T, U	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, M, R	4		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth G], BA [auth G], CA [auth G], DA [auth G], EA [auth G], FA [auth B], GA [auth F], HA [auth F], IA [auth F], JA [auth F], KA [auth F], LA [auth F], MA [auth F], NA [auth F], OA [auth F], PA [auth A], QA [auth E], RA [auth E], SA [auth E], TA [auth E], UA [auth E], V [auth C], VA [auth E], W [auth G], WA [auth E], X [auth G], XA [auth E], Y [auth G], YA [auth E], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Gavor, E., Gristick, H.B., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HIVRAD P01 AI100148
Bill & Melinda Gates Foundation	United States	INV-070086

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release