9NVW | pdb_00009nvw

Cryo-EM structure of rhesus antibody CH35-Apex1.08 in complex with HIV Env trimer Q23-APEX-GT2

PDB DOI: https://doi.org/10.2210/pdb9NVW/pdb
EM Map EMD-49866: EMDB EMDataResource

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

Deposited: 2025-03-21 Released: 2026-04-01
Deposition Author(s): Roark, R.S., Shapiro, L.S., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques.

Mishra, N., Liang, B., Roark, R.S., Ghosh, A.R., Callaghan, S., Lee, W.H., Li, X., Vo, A.L., Avillion, G., Chowdhury, R.R., Habib, R., Bibollet-Ruche, F., Giese, G., Oberoi, P., Amereh, K., Somanathan, A., Zhu, Y., Zhang, Y., Kassab, M., Tjio, L., Andrabi, S., Reyes, R.A., Allen, J.D., James, N.E., Randall Jr., K.N., van der Maas, L., Ben-Akiva, E., Kacmarek-Michaels, K., Plante, S., Martella, C.L., Skelly, A.N., Singh, A., Hurtado, J., Dueker, K., Capozzola, T., Nedellec, R., Ozorowski, G., Lewis, M.G., Falcone, S., Carfi, A., Himansu, S., Shapiro, L., Crispin, M., Hahn, B.H., Briney, B., Irvine, D.J., Burton, D.R., Ward, A.B., Batista, F.D., Kwong, P.D., Shaw, G.M., Andrabi, R.

(2026) Immunity 59: 1140-1160.e11

PubMed: 41985438 Search on PubMed
DOI: https://doi.org/10.1016/j.immuni.2026.03.012
Primary Citation Related Structures:
9NVV, 9NVW, 9NVX, 9NVY, 9NVZ, 9NW0, 9NW1

PubMed Abstract:
Germline targeting (GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been achieved. Using antibody-guided structure-based design, we engineered a GT HIV trimer immunogen, Q23-APEX-GT2, which primes diverse V2-apex bnAb precursors. Q23-APEX-GT2 efficiently activated rare V2-apex-specific B cells in humanized knockin mice and consistently elicited immunofocused antibody responses in outbred rhesus macaques, priming multiple long heavy-chain complementarity-determining region 3 (CDRH3)-loop bnAb-B cell lineages. Monoclonal antibodies isolated from immunized macaques showed broad heterologous HIV trimer recognition and modest cross-neutralization of diverse tier-2 viruses. Cryoelectron microscopy (cryo-EM) structural studies confirmed precise epitope targeting and revealed CDRH3-mediated binding modes that mirrored those of human V2-apex bnAbs. Together, these findings establish proof of principle for priming and early maturation of authentic V2-apex bnAb precursors in outbred macaques and highlight the promise of V2-apex-targeted HIV vaccines.

Organizational Affiliation

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.

Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Immunology, Harvard Medical School, Harvard University, Cambridge, MA 02114, USA.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Bioqual, Inc., Rockville, MD, USA.

Moderna, Inc., Cambridge, MA 02139, USA.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Immunology, Harvard Medical School, Harvard University, Cambridge, MA 02114, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.

Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Immunology, Harvard Medical School, Harvard University, Cambridge, MA 02114, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: fbatista1@mgh.harvard.edu.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: raiees.andrabi@pennmedicine.upenn.edu.

Macromolecule Content

Total Structure Weight: 288.14 kDa
Atom Count: 17,222
Modeled Residue Count: 1,955
Deposited Residue Count: 2,353
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CH35-Apex1.08 heavy chain	A [auth H]	246	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CH35-Apex1.08 kappa chain	B [auth L]	214	Macaca mulatta	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV envelope gp120	C [auth b], E [auth d], G [auth f]	478	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 20	Glycosylation Focus chain C [auth b] Focus chain E [auth d] Focus chain G [auth f]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV envelope gp41 ectodomain	D [auth c], F [auth e], H [auth g]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain D [auth c] Focus chain F [auth e] Focus chain H [auth g]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth U], CA [auth W], DA [auth X], EA [auth Y], FA [auth Z], AA [auth U], CA [auth W], DA [auth X], EA [auth Y], FA [auth Z], GA [auth a], I [auth A], KA [auth k], L [auth D], LA [auth l], N [auth F], NA [auth n], O [auth G], OA [auth o], PA [auth p], Q [auth J], QA [auth q], R [auth K], S [auth M], SA [auth s], T [auth N], U [auth O], X [auth R], Y [auth S], Z [auth T]	2		N-Glycosylation	Interactions Focus chain AA [auth U] Focus chain CA [auth W] Focus chain DA [auth X] Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain I [auth A] Focus chain KA [auth k] Focus chain L [auth D] Focus chain LA [auth l] Focus chain N [auth F] Focus chain NA [auth n] Focus chain O [auth G] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth J] Focus chain QA [auth q] Focus chain R [auth K] Focus chain S [auth M] Focus chain SA [auth s] Focus chain T [auth N] Focus chain U [auth O] Focus chain X [auth R] Focus chain Y [auth S] Focus chain Z [auth T] Interactions & Density Focus chain AA [auth U] Focus chain CA [auth W] Focus chain DA [auth X] Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain I [auth A] Focus chain KA [auth k] Focus chain L [auth D] Focus chain LA [auth l] Focus chain N [auth F] Focus chain NA [auth n] Focus chain O [auth G] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth J] Focus chain QA [auth q] Focus chain R [auth K] Focus chain S [auth M] Focus chain SA [auth s] Focus chain T [auth N] Focus chain U [auth O] Focus chain X [auth R] Focus chain Y [auth S] Focus chain Z [auth T]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth V], HA [auth h], J [auth B], JA [auth j], K [auth C], BA [auth V], HA [auth h], J [auth B], JA [auth j], K [auth C], MA [auth m], P [auth I], V [auth P]	3		N-Glycosylation	Interactions Focus chain BA [auth V] Focus chain HA [auth h] Focus chain J [auth B] Focus chain JA [auth j] Focus chain K [auth C] Focus chain MA [auth m] Focus chain P [auth I] Focus chain V [auth P] Interactions & Density Focus chain BA [auth V] Focus chain HA [auth h] Focus chain J [auth B] Focus chain JA [auth j] Focus chain K [auth C] Focus chain MA [auth m] Focus chain P [auth I] Focus chain V [auth P]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-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	M [auth E]	5		N-Glycosylation	Interactions Focus chain M [auth E] Interactions & Density Focus chain M [auth E]
Glycosylation Resources
GlyTouCan: G77367MI GlyCosmos: G77367MI GlyGen: G77367MI

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	IA [auth i], RA [auth r], W [auth Q]	5		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain RA [auth r] Focus chain W [auth Q] Interactions & Density Focus chain IA [auth i] Focus chain RA [auth r] Focus chain W [auth Q]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth b] SDF format, chain YB [auth g] SDF format, chain YA [auth b] SDF format, chain XB [auth g] SDF format, chain XA [auth b] SDF format, chain WB [auth g] SDF format, chain WA [auth b] SDF format, chain VB [auth f] SDF format, chain VA [auth b] SDF format, chain UB [auth f] SDF format, chain UA [auth b] SDF format, chain TB [auth f] SDF format, chain TA [auth b] SDF format, chain SB [auth f] SDF format, chain RB [auth f] SDF format, chain QB [auth f] SDF format, chain PB [auth f] SDF format, chain OB [auth e] SDF format, chain NB [auth e] SDF format, chain MB [auth e] SDF format, chain LB [auth d] SDF format, chain KB [auth d] SDF format, chain JB [auth d] SDF format, chain IB [auth d] SDF format, chain HB [auth d] SDF format, chain GB [auth d] SDF format, chain FB [auth d] SDF format, chain EB [auth d] SDF format, chain DB [auth c] SDF format, chain CB [auth c] SDF format, chain BB [auth c] SDF format, chain AB [auth b] MOL2 format, chain ZA [auth b] MOL2 format, chain YB [auth g] MOL2 format, chain YA [auth b] MOL2 format, chain XB [auth g] MOL2 format, chain XA [auth b] MOL2 format, chain WB [auth g] MOL2 format, chain WA [auth b] MOL2 format, chain VB [auth f] MOL2 format, chain VA [auth b] MOL2 format, chain UB [auth f] MOL2 format, chain UA [auth b] MOL2 format, chain TB [auth f] MOL2 format, chain TA [auth b] MOL2 format, chain SB [auth f] MOL2 format, chain RB [auth f] MOL2 format, chain QB [auth f] MOL2 format, chain PB [auth f] MOL2 format, chain OB [auth e] MOL2 format, chain NB [auth e] MOL2 format, chain MB [auth e] MOL2 format, chain LB [auth d] MOL2 format, chain KB [auth d] MOL2 format, chain JB [auth d] MOL2 format, chain IB [auth d] MOL2 format, chain HB [auth d] MOL2 format, chain GB [auth d] MOL2 format, chain FB [auth d] MOL2 format, chain EB [auth d] MOL2 format, chain DB [auth c] MOL2 format, chain CB [auth c] MOL2 format, chain BB [auth c] MOL2 format, chain AB [auth b] mmCIF format, chain ZA [auth b] mmCIF format, chain YB [auth g] mmCIF format, chain YA [auth b] mmCIF format, chain XB [auth g] mmCIF format, chain XA [auth b] mmCIF format, chain WB [auth g] mmCIF format, chain WA [auth b] mmCIF format, chain VB [auth f] mmCIF format, chain VA [auth b] mmCIF format, chain UB [auth f] mmCIF format, chain UA [auth b] mmCIF format, chain TB [auth f] mmCIF format, chain TA [auth b] mmCIF format, chain SB [auth f] mmCIF format, chain RB [auth f] mmCIF format, chain QB [auth f] mmCIF format, chain PB [auth f] mmCIF format, chain OB [auth e] mmCIF format, chain NB [auth e] mmCIF format, chain MB [auth e] mmCIF format, chain LB [auth d] mmCIF format, chain KB [auth d] mmCIF format, chain JB [auth d] mmCIF format, chain IB [auth d] mmCIF format, chain HB [auth d] mmCIF format, chain GB [auth d] mmCIF format, chain FB [auth d] mmCIF format, chain EB [auth d] mmCIF format, chain DB [auth c] mmCIF format, chain CB [auth c] mmCIF format, chain BB [auth c] mmCIF format, chain AB [auth b]	AB [auth b] BB [auth c] CB [auth c] DB [auth c] EB [auth d] AB [auth b], BB [auth c], CB [auth c], DB [auth c], EB [auth d], FB [auth d], GB [auth d], HB [auth d], IB [auth d], JB [auth d], KB [auth d], LB [auth d], MB [auth e], NB [auth e], OB [auth e], PB [auth f], QB [auth f], RB [auth f], SB [auth f], TA [auth b], TB [auth f], UA [auth b], UB [auth f], VA [auth b], VB [auth f], WA [auth b], WB [auth g], XA [auth b], XB [auth g], YA [auth b], YB [auth g], ZA [auth b]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth b] Focus chain BB [auth c] Focus chain CB [auth c] Focus chain DB [auth c] Focus chain EB [auth d] Focus chain FB [auth d] Focus chain GB [auth d] Focus chain HB [auth d] Focus chain IB [auth d] Focus chain JB [auth d] Focus chain KB [auth d] Focus chain LB [auth d] Focus chain MB [auth e] Focus chain NB [auth e] Focus chain OB [auth e] Focus chain PB [auth f] Focus chain QB [auth f] Focus chain RB [auth f] Focus chain SB [auth f] Focus chain TA [auth b] Focus chain TB [auth f] Focus chain UA [auth b] Focus chain UB [auth f] Focus chain VA [auth b] Focus chain VB [auth f] Focus chain WA [auth b] Focus chain WB [auth g] Focus chain XA [auth b] Focus chain XB [auth g] Focus chain YA [auth b] Focus chain YB [auth g] Focus chain ZA [auth b] Interactions & Density Focus chain AB [auth b] Focus chain BB [auth c] Focus chain CB [auth c] Focus chain DB [auth c] Focus chain EB [auth d] Focus chain FB [auth d] Focus chain GB [auth d] Focus chain HB [auth d] Focus chain IB [auth d] Focus chain JB [auth d] Focus chain KB [auth d] Focus chain LB [auth d] Focus chain MB [auth e] Focus chain NB [auth e] Focus chain OB [auth e] Focus chain PB [auth f] Focus chain QB [auth f] Focus chain RB [auth f] Focus chain SB [auth f] Focus chain TA [auth b] Focus chain TB [auth f] Focus chain UA [auth b] Focus chain UB [auth f] Focus chain VA [auth b] Focus chain VB [auth f] Focus chain WA [auth b] Focus chain WB [auth g] Focus chain XA [auth b] Focus chain XB [auth g] Focus chain YA [auth b] Focus chain YB [auth g] Focus chain ZA [auth b]