9OOM | pdb_00009oom

Cryo-EM structure of vaccine-elicited antibody T6_P_H03 in complex with HIV Env trimer Q23-APEX-GT1

PDB DOI: https://doi.org/10.2210/pdb9OOM/pdb
EM Map EMD-70666: EMDB EMDataResource

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

Deposited: 2025-05-16 Released: 2025-11-12
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: 3.50 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

Rapidly acquired HIV-1 neutralization breadth in a rhesus V2 apex knockin mouse model after a single bolus immunization.

Ghosh, A.R., Habib, R., Mishra, N., Roark, R.S., Akauliya, M., Albowaidey, A.A., Allen, J.D., Amereh, K., Avillion, G., Bottermann, M., Liang, B., Chaudhary, N., Callaghan, S., Dye, J., Li, X., Ellis-Pugh, J.R., Roy Chowdhury, R., James, N.E., Liu, X., Maiorino, L., Villavicencio, P.M., Nedellec, R., Oberoi, P., Sowers, K.J., Park, Y., Prum, T., Rodriguez, L., Ssozi, M., Torres, J.L., Walsh, A.A., Warner, J.E., Weldon, S.R., Xu, L., Wiehe, K., Crispin, M., Ward, A.B., Nair, U., Hahn, B.H., Burton, D.R., Shapiro, L., Kwong, P.D., Irvine, D.J., Andrabi, R., Shaw, G.M., Batista, F.D.

(2026) Sci Immunol 11: eadz5064-eadz5064

PubMed: 41686913 Search on PubMed
DOI: https://doi.org/10.1126/sciimmunol.adz5064
Primary Citation of Related Structures:
9OOG, 9OOK, 9OOM

PubMed Abstract:
Current immunization strategies to elicit broadly neutralizing antibodies (bnAbs) against HIV-1 generally propose complex, multiboost regimens. In rhesus macaques, simian-human immunodeficiency virus (SHIV) infection rapidly drives the development of some bnAb classes sharing structural similarities with those in humans. Here, we generated a knockin (KI) mouse model with B cells bearing the unmutated common ancestor of a V2 apex-targeted bnAb lineage, V033-a. A single immunization with a germline-targeting native-like trimer, Q23-APEX-GT1, recapitulated the ontogeny of the mature rhesus bnAb in KI mice, including rare, disfavored somatic mutations. Resulting antibodies exhibited potent neutralization against a broad panel of heterologous HIV-1 strains. Boosting with Env escape mutant trimers further improved breadth and potency, and cryo-electron microscopy analysis revealed the structural basis for heterologous neutralization breadth. Nonhuman primate and mouse models combined with structure can serve as a platform for identifying and validating immunogens that streamline HIV vaccination regimens.

Organizational Affiliation

Batista Lab, Ragon Institute of Mass General Brigham, MIT, and Harvard, Cambridge, MA 02139, USA.

Macromolecule Content

Total Structure Weight: 396.86 kDa
Atom Count: 21,059
Modeled Residue Count: 2,433
Deposited Residue Count: 3,315
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T6_P_H03 heavy chain	A [auth H], I, K [auth J]	235	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T6_P_H03 light chain	B [auth L], J [auth M], L [auth N]	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Env gp120	C [auth b], E [auth d], G [auth f]	503	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Env gp41 ectodomain	D [auth c], F [auth e], H [auth g]	153	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth Y], FA [auth Z], GA [auth a], HA [auth h], IA [auth i], EA [auth Y], FA [auth Z], GA [auth a], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], M [auth A], MA [auth m], R [auth F], RA [auth r], S [auth G], SA [auth s], T [auth K], TA [auth t], U [auth O], UA [auth u], V [auth P], VA [auth v], W [auth Q], WA [auth w], X [auth R], XA [auth x], Y [auth S], YA [auth y], Z [auth T]	2		N-Glycosylation	Interactions Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth A] Focus chain MA [auth m] Focus chain R [auth F] Focus chain RA [auth r] Focus chain S [auth G] Focus chain SA [auth s] Focus chain T [auth K] Focus chain TA [auth t] Focus chain U [auth O] Focus chain UA [auth u] Focus chain V [auth P] Focus chain VA [auth v] Focus chain W [auth Q] Focus chain WA [auth w] Focus chain X [auth R] Focus chain XA [auth x] Focus chain Y [auth S] Focus chain YA [auth y] Focus chain Z [auth T] Interactions & Density Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth A] Focus chain MA [auth m] Focus chain R [auth F] Focus chain RA [auth r] Focus chain S [auth G] Focus chain SA [auth s] Focus chain T [auth K] Focus chain TA [auth t] Focus chain U [auth O] Focus chain UA [auth u] Focus chain V [auth P] Focus chain VA [auth v] Focus chain W [auth Q] Focus chain WA [auth w] Focus chain X [auth R] Focus chain XA [auth x] Focus chain Y [auth S] Focus chain YA [auth y] Focus chain Z [auth T]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth U], N [auth B], NA [auth n]	3		N-Glycosylation	Interactions Focus chain AA [auth U] Focus chain N [auth B] Focus chain NA [auth n] Interactions & Density Focus chain AA [auth U] Focus chain N [auth B] Focus chain NA [auth n]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	BA [auth V], O [auth C], OA [auth o]	5		N-Glycosylation	Interactions Focus chain BA [auth V] Focus chain O [auth C] Focus chain OA [auth o] Interactions & Density Focus chain BA [auth V] Focus chain O [auth C] Focus chain OA [auth o]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	P [auth D]	5		N-Glycosylation	Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
Glycosylation Resources
GlyTouCan: G10756ZZ GlyCosmos: G10756ZZ GlyGen: G10756ZZ

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	Q [auth E], QA [auth q]	8		N-Glycosylation	Interactions Focus chain Q [auth E] Focus chain QA [auth q] Interactions & Density Focus chain Q [auth E] Focus chain QA [auth q]
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-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	CA [auth W], PA [auth p]	5		N-Glycosylation	Interactions Focus chain CA [auth W] Focus chain PA [auth p] Interactions & Density Focus chain CA [auth W] Focus chain PA [auth p]
Glycosylation Resources
GlyTouCan: G94626GC GlyCosmos: G94626GC GlyGen: G94626GC

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	DA [auth X]	6		N-Glycosylation	Interactions Focus chain DA [auth X] Interactions & Density Focus chain DA [auth X]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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 ZB [auth f] SDF format, chain ZA [auth b] SDF format, chain YB [auth f] SDF format, chain XB [auth f] SDF format, chain WB [auth f] SDF format, chain VB [auth f] SDF format, chain UB [auth f] SDF format, chain TB [auth f] SDF format, chain SB [auth e] SDF format, chain RB [auth e] SDF format, chain QB [auth e] SDF format, chain PB [auth d] SDF format, chain OB [auth d] SDF format, chain NB [auth d] SDF format, chain MB [auth d] SDF format, chain LB [auth d] SDF format, chain KB [auth d] SDF format, chain JB [auth d] SDF format, chain IB [auth c] SDF format, chain HB [auth c] SDF format, chain GB [auth c] SDF format, chain FB [auth b] SDF format, chain EB [auth b] SDF format, chain DB [auth b] SDF format, chain CC [auth g] SDF format, chain CB [auth b] SDF format, chain BC [auth g] SDF format, chain BB [auth b] SDF format, chain AC [auth g] SDF format, chain AB [auth b] MOL2 format, chain ZB [auth f] MOL2 format, chain ZA [auth b] MOL2 format, chain YB [auth f] MOL2 format, chain XB [auth f] MOL2 format, chain WB [auth f] MOL2 format, chain VB [auth f] MOL2 format, chain UB [auth f] MOL2 format, chain TB [auth f] MOL2 format, chain SB [auth e] MOL2 format, chain RB [auth e] MOL2 format, chain QB [auth e] MOL2 format, chain PB [auth d] MOL2 format, chain OB [auth d] MOL2 format, chain NB [auth d] MOL2 format, chain MB [auth d] MOL2 format, chain LB [auth d] MOL2 format, chain KB [auth d] MOL2 format, chain JB [auth d] MOL2 format, chain IB [auth c] MOL2 format, chain HB [auth c] MOL2 format, chain GB [auth c] MOL2 format, chain FB [auth b] MOL2 format, chain EB [auth b] MOL2 format, chain DB [auth b] MOL2 format, chain CC [auth g] MOL2 format, chain CB [auth b] MOL2 format, chain BC [auth g] MOL2 format, chain BB [auth b] MOL2 format, chain AC [auth g] MOL2 format, chain AB [auth b] mmCIF format, chain ZB [auth f] mmCIF format, chain ZA [auth b] mmCIF format, chain YB [auth f] mmCIF format, chain XB [auth f] mmCIF format, chain WB [auth f] mmCIF format, chain VB [auth f] mmCIF format, chain UB [auth f] mmCIF format, chain TB [auth f] mmCIF format, chain SB [auth e] mmCIF format, chain RB [auth e] mmCIF format, chain QB [auth e] mmCIF format, chain PB [auth d] mmCIF format, chain OB [auth d] mmCIF format, chain NB [auth d] mmCIF format, chain MB [auth d] mmCIF format, chain LB [auth d] mmCIF format, chain KB [auth d] mmCIF format, chain JB [auth d] mmCIF format, chain IB [auth c] mmCIF format, chain HB [auth c] mmCIF format, chain GB [auth c] mmCIF format, chain FB [auth b] mmCIF format, chain EB [auth b] mmCIF format, chain DB [auth b] mmCIF format, chain CC [auth g] mmCIF format, chain CB [auth b] mmCIF format, chain BC [auth g] mmCIF format, chain BB [auth b] mmCIF format, chain AC [auth g] mmCIF format, chain AB [auth b]	AB [auth b] AC [auth g] BB [auth b] BC [auth g] CB [auth b] AB [auth b], AC [auth g], BB [auth b], BC [auth g], CB [auth b], CC [auth g], DB [auth b], EB [auth b], FB [auth b], GB [auth c], HB [auth c], IB [auth c], JB [auth d], KB [auth d], LB [auth d], MB [auth d], NB [auth d], OB [auth d], PB [auth d], QB [auth e], RB [auth e], SB [auth e], TB [auth f], UB [auth f], VB [auth f], WB [auth f], XB [auth f], YB [auth f], ZA [auth b], ZB [auth f]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth b] Focus chain AC [auth g] Focus chain BB [auth b] Focus chain BC [auth g] Focus chain CB [auth b] Focus chain CC [auth g] Focus chain DB [auth b] Focus chain EB [auth b] Focus chain FB [auth b] Focus chain GB [auth c] Focus chain HB [auth c] Focus chain IB [auth c] Focus chain JB [auth d] Focus chain KB [auth d] Focus chain LB [auth d] Focus chain MB [auth d] Focus chain NB [auth d] Focus chain OB [auth d] Focus chain PB [auth d] Focus chain QB [auth e] Focus chain RB [auth e] Focus chain SB [auth e] Focus chain TB [auth f] Focus chain UB [auth f] Focus chain VB [auth f] Focus chain WB [auth f] Focus chain XB [auth f] Focus chain YB [auth f] Focus chain ZA [auth b] Focus chain ZB [auth f] Interactions & Density Focus chain AB [auth b] Focus chain AC [auth g] Focus chain BB [auth b] Focus chain BC [auth g] Focus chain CB [auth b] Focus chain CC [auth g] Focus chain DB [auth b] Focus chain EB [auth b] Focus chain FB [auth b] Focus chain GB [auth c] Focus chain HB [auth c] Focus chain IB [auth c] Focus chain JB [auth d] Focus chain KB [auth d] Focus chain LB [auth d] Focus chain MB [auth d] Focus chain NB [auth d] Focus chain OB [auth d] Focus chain PB [auth d] Focus chain QB [auth e] Focus chain RB [auth e] Focus chain SB [auth e] Focus chain TB [auth f] Focus chain UB [auth f] Focus chain VB [auth f] Focus chain WB [auth f] Focus chain XB [auth f] Focus chain YB [auth f] Focus chain ZA [auth b] Focus chain ZB [auth f]