9Q3S | pdb_00009q3s

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

PDB DOI: https://doi.org/10.2210/pdb9Q3S/pdb
EM Map EMD-72206: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Macaca mulatta, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-08-19 Released: 2026-05-27
Deposition Author(s): Chandravanshi, M., Tolbert, W.D., Pazgier, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.01 Å
Resolution: 3.01 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

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

Chandravanshi, M., Tolbert, W.D., Pazgier, M.

To be published.

Macromolecule Content

Total Structure Weight: 528.34 kDa
Atom Count: 26,619
Modeled Residue Count: 3,138
Deposited Residue Count: 4,578
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.664 gp41	A [auth B], G [auth C], M [auth J]	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S5
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth B] Focus chain G [auth C] Focus chain M [auth J]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.664 gp120	B [auth G], H [auth A], N [auth I]	481	Human immunodeficiency virus 1	Mutation(s): 4 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S5
Glycosylation
Glycosylation Sites: 19	Glycosylation Focus chain B [auth G] Focus chain H [auth A] Focus chain N [auth I]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ab 4 Fab heavy chain	C [auth H], I [auth D], O [auth K]	229	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ab 4 Fab light chain	D [auth L], J [auth E], P [auth M]	215	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT121 Fab heavy chain	E [auth h], K [auth d], Q [auth k]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT121 Fab light chain	F [auth l], L [auth e], R [auth m]	213	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 7
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	GA [auth b], S [auth N], UA [auth v]	4		N-Glycosylation	Interactions Focus chain GA [auth b] Focus chain S [auth N] Focus chain UA [auth v] Interactions & Density Focus chain GA [auth b] Focus chain S [auth N] Focus chain UA [auth v]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
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	HA [auth c], T [auth O], VA [auth w]	3		N-Glycosylation	Interactions Focus chain HA [auth c] Focus chain T [auth O] Focus chain VA [auth w] Interactions & Density Focus chain HA [auth c] Focus chain T [auth O] Focus chain VA [auth w]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
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 V], AB [auth 1], BA [auth W], BB [auth 2], CA [auth X], AA [auth V], AB [auth 1], BA [auth W], BB [auth 2], CA [auth X], CB [auth 3], DB [auth 4], EA [auth Z], EB [auth 5], FA [auth a], GB [auth 7], HB [auth 8], IA [auth f], JA [auth g], KA [auth i], MA [auth n], NA [auth o], OA [auth p], PA [auth q], QA [auth r], SA [auth t], TA [auth u], U [auth P], V [auth Q], W [auth R], WA [auth x], XA [auth y], Y [auth T], YA [auth z], Z [auth U]	2		N-Glycosylation	Interactions Focus chain AA [auth V] Focus chain AB [auth 1] Focus chain BA [auth W] Focus chain BB [auth 2] Focus chain CA [auth X] Focus chain CB [auth 3] Focus chain DB [auth 4] Focus chain EA [auth Z] Focus chain EB [auth 5] Focus chain FA [auth a] Focus chain GB [auth 7] Focus chain HB [auth 8] Focus chain IA [auth f] Focus chain JA [auth g] Focus chain KA [auth i] Focus chain MA [auth n] Focus chain NA [auth o] Focus chain OA [auth p] Focus chain PA [auth q] Focus chain QA [auth r] Focus chain SA [auth t] Focus chain TA [auth u] Focus chain U [auth P] Focus chain V [auth Q] Focus chain W [auth R] Focus chain WA [auth x] Focus chain XA [auth y] Focus chain Y [auth T] Focus chain YA [auth z] Focus chain Z [auth U] Interactions & Density Focus chain AA [auth V] Focus chain AB [auth 1] Focus chain BA [auth W] Focus chain BB [auth 2] Focus chain CA [auth X] Focus chain CB [auth 3] Focus chain DB [auth 4] Focus chain EA [auth Z] Focus chain EB [auth 5] Focus chain FA [auth a] Focus chain GB [auth 7] Focus chain HB [auth 8] Focus chain IA [auth f] Focus chain JA [auth g] Focus chain KA [auth i] Focus chain MA [auth n] Focus chain NA [auth o] Focus chain OA [auth p] Focus chain PA [auth q] Focus chain QA [auth r] Focus chain SA [auth t] Focus chain TA [auth u] Focus chain U [auth P] Focus chain V [auth Q] Focus chain W [auth R] Focus chain WA [auth x] Focus chain XA [auth y] Focus chain Y [auth T] Focus chain YA [auth z] Focus chain Z [auth U]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	LA [auth j], X [auth S], ZA [auth 0]	6		N-Glycosylation	Interactions Focus chain LA [auth j] Focus chain X [auth S] Focus chain ZA [auth 0] Interactions & Density Focus chain LA [auth j] Focus chain X [auth S] Focus chain ZA [auth 0]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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	DA [auth Y], FB [auth 6], RA [auth s]	9		N-Glycosylation	Interactions Focus chain DA [auth Y] Focus chain FB [auth 6] Focus chain RA [auth s] Interactions & Density Focus chain DA [auth Y] Focus chain FB [auth 6] Focus chain RA [auth s]
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

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 AC [auth I] SDF format, chain LB [auth G] SDF format, chain NB [auth G] SDF format, chain PB [auth C] SDF format, chain RB [auth A] SDF format, chain SB [auth A] SDF format, chain TB [auth A] SDF format, chain UB [auth A] SDF format, chain YB [auth I] SDF format, chain ZB [auth I] SDF format, chain XB [auth J] SDF format, chain WB [auth J] SDF format, chain VB [auth A] SDF format, chain QB [auth C] SDF format, chain OB [auth G] SDF format, chain MB [auth G] SDF format, chain KB [auth G] SDF format, chain JB [auth B] SDF format, chain IB [auth B] SDF format, chain CC [auth I] SDF format, chain BC [auth I] MOL2 format, chain AC [auth I] MOL2 format, chain LB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain PB [auth C] MOL2 format, chain RB [auth A] MOL2 format, chain SB [auth A] MOL2 format, chain TB [auth A] MOL2 format, chain UB [auth A] MOL2 format, chain YB [auth I] MOL2 format, chain ZB [auth I] MOL2 format, chain XB [auth J] MOL2 format, chain WB [auth J] MOL2 format, chain VB [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain OB [auth G] MOL2 format, chain MB [auth G] MOL2 format, chain KB [auth G] MOL2 format, chain JB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain CC [auth I] MOL2 format, chain BC [auth I] mmCIF format, chain AC [auth I] mmCIF format, chain LB [auth G] mmCIF format, chain NB [auth G] mmCIF format, chain PB [auth C] mmCIF format, chain RB [auth A] mmCIF format, chain SB [auth A] mmCIF format, chain TB [auth A] mmCIF format, chain UB [auth A] mmCIF format, chain YB [auth I] mmCIF format, chain ZB [auth I] mmCIF format, chain XB [auth J] mmCIF format, chain WB [auth J] mmCIF format, chain VB [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain OB [auth G] mmCIF format, chain MB [auth G] mmCIF format, chain KB [auth G] mmCIF format, chain JB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain CC [auth I] mmCIF format, chain BC [auth I]	AC [auth I] BC [auth I] CC [auth I] IB [auth B] JB [auth B] AC [auth I], BC [auth I], CC [auth I], IB [auth B], JB [auth B], KB [auth G], LB [auth G], MB [auth G], NB [auth G], OB [auth G], PB [auth C], QB [auth C], RB [auth A], SB [auth A], TB [auth A], UB [auth A], VB [auth A], WB [auth J], XB [auth J], YB [auth I], ZB [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AC [auth I] Focus chain BC [auth I] Focus chain CC [auth I] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth G] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth C] Focus chain QB [auth C] Focus chain RB [auth A] Focus chain SB [auth A] Focus chain TB [auth A] Focus chain UB [auth A] Focus chain VB [auth A] Focus chain WB [auth J] Focus chain XB [auth J] Focus chain YB [auth I] Focus chain ZB [auth I] Interactions & Density Focus chain AC [auth I] Focus chain BC [auth I] Focus chain CC [auth I] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth G] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth C] Focus chain QB [auth C] Focus chain RB [auth A] Focus chain SB [auth A] Focus chain TB [auth A] Focus chain UB [auth A] Focus chain VB [auth A] Focus chain WB [auth J] Focus chain XB [auth J] Focus chain YB [auth I] Focus chain ZB [auth I]