9OOK | pdb_00009ook

Cryo-EM structure of vaccine-elicited antibody T3_QB_G12 in complex with HIV Env trimer Q23-APEX-GT1

PDB DOI: https://doi.org/10.2210/pdb9OOK/pdb
EM Map EMD-70664: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-15 Released: 2025-11-05
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: 3.80 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

Amrit, G., Roark, R.S., Kwong, P.D., Batista, F.D.

To be published.

Macromolecule Content

Total Structure Weight: 394.75 kDa
Atom Count: 20,928
Modeled Residue Count: 2,430
Deposited Residue Count: 3,312
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T3_QB_G12 heavy chain	A [auth H], E [auth I], I [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
T3_QB_G12 light chain	B [auth L], F [auth M], J [auth N]	213	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 f], G [auth h], K [auth j]	503	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 20	Glycosylation Focus chain C [auth f] Focus chain G [auth h] Focus chain K [auth j]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Env gp41 ectodomain	D [auth g], H [auth i], L [auth k]	153	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain D [auth g] Focus chain H [auth i] Focus chain L [auth k]
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 b], IA [auth c], EA [auth Y], FA [auth Z], GA [auth a], HA [auth b], IA [auth c], JA [auth d], KA [auth e], 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 b] Focus chain IA [auth c] Focus chain JA [auth d] Focus chain KA [auth e] 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 b] Focus chain IA [auth c] Focus chain JA [auth d] Focus chain KA [auth e] 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], CA [auth W], N [auth B], NA [auth n], P [auth D], AA [auth U], CA [auth W], N [auth B], NA [auth n], P [auth D], PA [auth p]	3		N-Glycosylation	Interactions Focus chain AA [auth U] Focus chain CA [auth W] Focus chain N [auth B] Focus chain NA [auth n] Focus chain P [auth D] Focus chain PA [auth p] Interactions & Density Focus chain AA [auth U] Focus chain CA [auth W] Focus chain N [auth B] Focus chain NA [auth n] Focus chain P [auth D] Focus chain PA [auth p]
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], DA [auth X], O [auth C], OA [auth o], Q [auth E], BA [auth V], DA [auth X], O [auth C], OA [auth o], Q [auth E], QA [auth q]	5		N-Glycosylation	Interactions Focus chain BA [auth V] Focus chain DA [auth X] Focus chain O [auth C] Focus chain OA [auth o] Focus chain Q [auth E] Focus chain QA [auth q] Interactions & Density Focus chain BA [auth V] Focus chain DA [auth X] Focus chain O [auth C] Focus chain OA [auth o] Focus chain Q [auth E] Focus chain QA [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 ZB [auth j] SDF format, chain ZA [auth f] SDF format, chain YB [auth j] SDF format, chain XB [auth j] SDF format, chain WB [auth j] SDF format, chain VB [auth j] SDF format, chain UB [auth j] SDF format, chain TB [auth j] SDF format, chain SB [auth i] SDF format, chain RB [auth i] SDF format, chain QB [auth i] SDF format, chain PB [auth h] SDF format, chain OB [auth h] SDF format, chain NB [auth h] SDF format, chain MB [auth h] SDF format, chain LB [auth h] SDF format, chain KB [auth h] SDF format, chain JB [auth h] SDF format, chain IB [auth g] SDF format, chain HB [auth g] SDF format, chain GB [auth g] SDF format, chain FB [auth f] SDF format, chain EB [auth f] SDF format, chain DB [auth f] SDF format, chain CC [auth k] SDF format, chain CB [auth f] SDF format, chain BC [auth k] SDF format, chain BB [auth f] SDF format, chain AC [auth k] SDF format, chain AB [auth f] MOL2 format, chain ZB [auth j] MOL2 format, chain ZA [auth f] MOL2 format, chain YB [auth j] MOL2 format, chain XB [auth j] MOL2 format, chain WB [auth j] MOL2 format, chain VB [auth j] MOL2 format, chain UB [auth j] MOL2 format, chain TB [auth j] MOL2 format, chain SB [auth i] MOL2 format, chain RB [auth i] MOL2 format, chain QB [auth i] MOL2 format, chain PB [auth h] MOL2 format, chain OB [auth h] MOL2 format, chain NB [auth h] MOL2 format, chain MB [auth h] MOL2 format, chain LB [auth h] MOL2 format, chain KB [auth h] MOL2 format, chain JB [auth h] MOL2 format, chain IB [auth g] MOL2 format, chain HB [auth g] MOL2 format, chain GB [auth g] MOL2 format, chain FB [auth f] MOL2 format, chain EB [auth f] MOL2 format, chain DB [auth f] MOL2 format, chain CC [auth k] MOL2 format, chain CB [auth f] MOL2 format, chain BC [auth k] MOL2 format, chain BB [auth f] MOL2 format, chain AC [auth k] MOL2 format, chain AB [auth f] mmCIF format, chain ZB [auth j] mmCIF format, chain ZA [auth f] mmCIF format, chain YB [auth j] mmCIF format, chain XB [auth j] mmCIF format, chain WB [auth j] mmCIF format, chain VB [auth j] mmCIF format, chain UB [auth j] mmCIF format, chain TB [auth j] mmCIF format, chain SB [auth i] mmCIF format, chain RB [auth i] mmCIF format, chain QB [auth i] mmCIF format, chain PB [auth h] mmCIF format, chain OB [auth h] mmCIF format, chain NB [auth h] mmCIF format, chain MB [auth h] mmCIF format, chain LB [auth h] mmCIF format, chain KB [auth h] mmCIF format, chain JB [auth h] mmCIF format, chain IB [auth g] mmCIF format, chain HB [auth g] mmCIF format, chain GB [auth g] mmCIF format, chain FB [auth f] mmCIF format, chain EB [auth f] mmCIF format, chain DB [auth f] mmCIF format, chain CC [auth k] mmCIF format, chain CB [auth f] mmCIF format, chain BC [auth k] mmCIF format, chain BB [auth f] mmCIF format, chain AC [auth k] mmCIF format, chain AB [auth f]	AB [auth f] AC [auth k] BB [auth f] BC [auth k] CB [auth f] AB [auth f], AC [auth k], BB [auth f], BC [auth k], CB [auth f], CC [auth k], DB [auth f], EB [auth f], FB [auth f], GB [auth g], HB [auth g], IB [auth g], JB [auth h], KB [auth h], LB [auth h], MB [auth h], NB [auth h], OB [auth h], PB [auth h], QB [auth i], RB [auth i], SB [auth i], TB [auth j], UB [auth j], VB [auth j], WB [auth j], XB [auth j], YB [auth j], ZA [auth f], ZB [auth j]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth f] Focus chain AC [auth k] Focus chain BB [auth f] Focus chain BC [auth k] Focus chain CB [auth f] Focus chain CC [auth k] Focus chain DB [auth f] Focus chain EB [auth f] Focus chain FB [auth f] Focus chain GB [auth g] Focus chain HB [auth g] Focus chain IB [auth g] Focus chain JB [auth h] Focus chain KB [auth h] Focus chain LB [auth h] Focus chain MB [auth h] Focus chain NB [auth h] Focus chain OB [auth h] Focus chain PB [auth h] Focus chain QB [auth i] Focus chain RB [auth i] Focus chain SB [auth i] Focus chain TB [auth j] Focus chain UB [auth j] Focus chain VB [auth j] Focus chain WB [auth j] Focus chain XB [auth j] Focus chain YB [auth j] Focus chain ZA [auth f] Focus chain ZB [auth j] Interactions & Density Focus chain AB [auth f] Focus chain AC [auth k] Focus chain BB [auth f] Focus chain BC [auth k] Focus chain CB [auth f] Focus chain CC [auth k] Focus chain DB [auth f] Focus chain EB [auth f] Focus chain FB [auth f] Focus chain GB [auth g] Focus chain HB [auth g] Focus chain IB [auth g] Focus chain JB [auth h] Focus chain KB [auth h] Focus chain LB [auth h] Focus chain MB [auth h] Focus chain NB [auth h] Focus chain OB [auth h] Focus chain PB [auth h] Focus chain QB [auth i] Focus chain RB [auth i] Focus chain SB [auth i] Focus chain TB [auth j] Focus chain UB [auth j] Focus chain VB [auth j] Focus chain WB [auth j] Focus chain XB [auth j] Focus chain YB [auth j] Focus chain ZA [auth f] Focus chain ZB [auth j]