9YJ0 | pdb_00009yj0

PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trimer and RM20A3 Fab

PDB DOI: https://doi.org/10.2210/pdb9YJ0/pdb
EM Map EMD-73007: EMDB EMDataResource

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

Deposited: 2025-10-03 Released: 2026-10-07
Deposition Author(s): Phulera, S., Omorodion, O., Ward, A.B., Ozorowski, G.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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

Tolerance of multiple glycan conformations by an N332-directed HIV bnAb lineage provides a roadmap to broad neutralization

Nemoz, B., Rouzeau, R.

To be published.

Macromolecule Content

Total Structure Weight: 541.38 kDa
Atom Count: 25,380
Modeled Residue Count: 3,069
Deposited Residue Count: 4,737
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 Fab heavy chain	A [auth I], G [auth M], M [auth Q]	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 light chain	B [auth G], H [auth J], N [auth O]	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P94_v18_c046 Chimera DS-SOSIP gp120	C [auth A], I [auth C], O [auth E]	500	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain C [auth A] Focus chain I [auth C] Focus chain O [auth E]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PC94-A.16 Fab heavy chain	D [auth H], J [auth K], P	234	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PC94-A.16 light chain	E [auth L], K [auth N], Q [auth R]	215	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
P94_v18_c046 Chimera DS-SOSIP gp41	F [auth B], L [auth D], R [auth F]	186	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain F [auth B] Focus chain L [auth D] Focus chain R [auth F]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 7
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	AA [auth a], BA [auth b], IA [auth i], JA [auth j], S, AA [auth a], BA [auth b], IA [auth i], JA [auth j], S, T	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain S Focus chain T Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], EA [auth e], FA [auth f], HA [auth h], KA [auth k], CA [auth c], EA [auth e], FA [auth f], HA [auth h], KA [auth k], MA [auth m], NA [auth n], PA [auth p], U, W, X, Z	2		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain PA [auth p] Focus chain U Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain PA [auth p] Focus chain U Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
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	DA [auth d], LA [auth l], V	4		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain LA [auth l] Focus chain V Interactions & Density Focus chain DA [auth d] Focus chain LA [auth l] Focus chain V
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
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-(1-2)-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	GA [auth g], OA [auth o], Y	9		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain OA [auth o] Focus chain Y Interactions & Density Focus chain GA [auth g] Focus chain OA [auth o] Focus chain Y
Glycosylation Resources
GlyTouCan: G04414GO GlyCosmos: G04414GO GlyGen: G04414GO

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 AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain JB [auth D] SDF format, chain KB [auth E] SDF format, chain LB [auth E] SDF format, chain MB [auth E] SDF format, chain NB [auth E] SDF format, chain OB [auth E] SDF format, chain PB [auth E] SDF format, chain QA [auth A] SDF format, chain QB [auth E] SDF format, chain RA [auth A] SDF format, chain RB [auth E] SDF format, chain SA [auth A] SDF format, chain SB [auth E] SDF format, chain TA [auth A] SDF format, chain TB [auth F] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain OB [auth E] MOL2 format, chain PB [auth E] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth E] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth E] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth E] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth F] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth D] mmCIF format, chain KB [auth E] mmCIF format, chain LB [auth E] mmCIF format, chain MB [auth E] mmCIF format, chain NB [auth E] mmCIF format, chain OB [auth E] mmCIF format, chain PB [auth E] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth E] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth E] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth E] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth F] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth B]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth D], KB [auth E], LB [auth E], MB [auth E], NB [auth E], OB [auth E], PB [auth E], QA [auth A], QB [auth E], RA [auth A], RB [auth E], SA [auth A], SB [auth E], TA [auth A], TB [auth F], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth D] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain PB [auth E] Focus chain QA [auth A] Focus chain QB [auth E] Focus chain RA [auth A] Focus chain RB [auth E] Focus chain SA [auth A] Focus chain SB [auth E] Focus chain TA [auth A] Focus chain TB [auth F] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth D] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain PB [auth E] Focus chain QA [auth A] Focus chain QB [auth E] Focus chain RA [auth A] Focus chain RB [auth E] Focus chain SA [auth A] Focus chain SB [auth E] Focus chain TA [auth A] Focus chain TB [auth F] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth B]