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 1.0 of the entry. See complete history.

Literature

Rapid acquisition of HIV-1 neutralization breadth in a rhesus V2 apex germline antibody mouse model with a single bolus priming immunization

Ghosh, A., Roark, R.S., Kwong, P.D., Batistia, F.D.

To be published.

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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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]