9PNU | pdb_00009pnu

Cryo-EM structure of K001-A1 Fab in complex with HIV-1 459C-OPT RnS DS-SOSIP Env trimer

PDB DOI: https://doi.org/10.2210/pdb9PNU/pdb
EM Map EMD-71772: EMDB EMDataResource

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

Deposited: 2025-07-21 Released: 2025-12-17
Deposition Author(s): Wang, S., Zhou, T., Kwong, P.D., Morano, N.C., Shapiro, L.
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
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

Dual Vaccine Elicitation of HIV-1 Neutralizing Antibodies against V2 Apex and Fusion Peptide

Duan, H., Nkolola, J.P., Wang, S., Kwong, P.D., Barouch, D.H., Zhou, T.

To be published.

Macromolecule Content

Total Structure Weight: 302.14 kDa
Atom Count: 19,422
Modeled Residue Count: 2,197
Deposited Residue Count: 2,413
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
K001-A1 Fab heavy chain	A [auth H]	246	Macaca mulatta	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
K001-A1 Fab light chain	B [auth L]	220	Macaca mulatta	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
459C-OPT probe RnS DS-SOSIP gp41	C [auth A], E [auth B], G [auth F]	179	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C [auth A] Focus chain E [auth B] Focus chain G [auth F]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
459C-OPT probe RnS DS-SOSIP gp120	D [auth C], F [auth G], H [auth I]	470	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain D [auth C] Focus chain F [auth G] Focus chain H [auth I]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 g], I [auth D], MA [auth m], Q	4		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain I [auth D] Focus chain MA [auth m] Focus chain Q Interactions & Density Focus chain GA [auth g] Focus chain I [auth D] Focus chain MA [auth m] Focus chain Q
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 a], CA [auth c], DA [auth d], FA [auth f], IA [auth i], AA [auth a], CA [auth c], DA [auth d], FA [auth f], IA [auth i], J [auth E], K [auth J], KA [auth k], L [auth K], N, NA [auth n], O, OA [auth o], P, PA [auth p], RA [auth r], S, TA [auth t], WA [auth w], Y, Z	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain J [auth E] Focus chain K [auth J] Focus chain KA [auth k] Focus chain L [auth K] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain RA [auth r] Focus chain S Focus chain TA [auth t] Focus chain WA [auth w] Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain J [auth E] Focus chain K [auth J] Focus chain KA [auth k] Focus chain L [auth K] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain RA [auth r] Focus chain S Focus chain TA [auth t] Focus chain WA [auth w] Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
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	BA [auth b], M, QA [auth q], T	6		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain M Focus chain QA [auth q] Focus chain T Interactions & Density Focus chain BA [auth b] Focus chain M Focus chain QA [auth q] Focus chain T
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 8
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 e], HA [auth h], LA [auth l], R, SA [auth s], EA [auth e], HA [auth h], LA [auth l], R, SA [auth s], U, V, VA [auth v], W, X, XA [auth x], YA [auth y]	2		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain HA [auth h] Focus chain LA [auth l] Focus chain R Focus chain SA [auth s] Focus chain U Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X Focus chain XA [auth x] Focus chain YA [auth y] Interactions & Density Focus chain EA [auth e] Focus chain HA [auth h] Focus chain LA [auth l] Focus chain R Focus chain SA [auth s] Focus chain U Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X Focus chain XA [auth x] Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
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	JA [auth j], UA [auth u]	5		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain UA [auth u] Interactions & Density Focus chain JA [auth j] Focus chain UA [auth u]
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 AB [auth A] SDF format, chain BB [auth A] SDF format, chain CB [auth A] 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 B] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth G] SDF format, chain MB [auth G] SDF format, chain NB [auth G] SDF format, chain OB [auth F] SDF format, chain PB [auth F] SDF format, chain QB [auth F] SDF format, chain RB [auth F] SDF format, chain SB [auth I] SDF format, chain TB [auth I] SDF format, chain UB [auth I] SDF format, chain VB [auth I] SDF format, chain WB [auth I] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CB [auth A] 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 B] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth G] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain OB [auth F] MOL2 format, chain PB [auth F] MOL2 format, chain QB [auth F] MOL2 format, chain RB [auth F] MOL2 format, chain SB [auth I] MOL2 format, chain TB [auth I] MOL2 format, chain UB [auth I] MOL2 format, chain VB [auth I] MOL2 format, chain WB [auth I] MOL2 format, chain ZA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain CB [auth A] 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 B] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth G] mmCIF format, chain MB [auth G] mmCIF format, chain NB [auth G] mmCIF format, chain OB [auth F] mmCIF format, chain PB [auth F] mmCIF format, chain QB [auth F] mmCIF format, chain RB [auth F] mmCIF format, chain SB [auth I] mmCIF format, chain TB [auth I] mmCIF format, chain UB [auth I] mmCIF format, chain VB [auth I] mmCIF format, chain WB [auth I] mmCIF format, chain ZA [auth A]	AB [auth A] BB [auth A] CB [auth A] DB [auth C] EB [auth C] AB [auth A], BB [auth A], CB [auth A], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth B], JB [auth B], KB [auth B], LB [auth G], MB [auth G], NB [auth G], OB [auth F], PB [auth F], QB [auth F], RB [auth F], SB [auth I], TB [auth I], UB [auth I], VB [auth I], WB [auth I], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] 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 B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain WB [auth I] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] 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 B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain WB [auth I] Focus chain ZA [auth A]