9PNN | pdb_00009pnn

Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer

PDB DOI: https://doi.org/10.2210/pdb9PNN/pdb
EM Map EMD-71767: EMDB EMDataResource

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

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: 3.50 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

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: 388.17 kDa
Atom Count: 21,225
Modeled Residue Count: 2,442
Deposited Residue Count: 3,225
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein BG505 DS-SOSIP gp41	A [auth B], E [auth A], I [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus type 1) Explore Q2N0S7 Go to UniProtKB: Q2N0S7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth B] Focus chain E [auth A] Focus chain I [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein BG505 DS-SOSIP gp120	B [auth G], F [auth C], J [auth I]	473	Human immunodeficiency virus 1	Mutation(s): 4 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain B [auth G] Focus chain F [auth C] Focus chain J [auth I]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody J601-A6 heavy chain	C [auth H], G [auth D], K [auth J]	234	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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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody J601-A6 light chain	D [auth L], H [auth E], L [auth K]	215	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-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]	4		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain M Focus chain QA [auth q] Interactions & Density Focus chain BA [auth b] Focus chain M Focus chain QA [auth q]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], EA [auth e], JA [auth j], N, P, CA [auth c], EA [auth e], JA [auth j], N, P, RA [auth r], TA [auth t], U, YA [auth y]	2		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain EA [auth e] Focus chain JA [auth j] Focus chain N Focus chain P Focus chain RA [auth r] Focus chain TA [auth t] Focus chain U Focus chain YA [auth y] Interactions & Density Focus chain CA [auth c] Focus chain EA [auth e] Focus chain JA [auth j] Focus chain N Focus chain P Focus chain RA [auth r] Focus chain TA [auth t] Focus chain U Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	DA [auth d], O, SA [auth s]	5		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain O Focus chain SA [auth s] Interactions & Density Focus chain DA [auth d] Focus chain O Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
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], AB [auth 0], CB [auth 2], DB [auth 3], EB [auth 4], AA [auth a], AB [auth 0], CB [auth 2], DB [auth 3], EB [auth 4], FA [auth f], HA [auth h], IA [auth i], KA [auth k], LA [auth l], NA [auth n], OA [auth o], PA [auth p], Q, S, T, UA [auth u], V, W, WA [auth w], XA [auth x], Y, Z, ZA [auth z]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q Focus chain S Focus chain T Focus chain UA [auth u] Focus chain V Focus chain W Focus chain WA [auth w] Focus chain XA [auth x] Focus chain Y Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q Focus chain S Focus chain T Focus chain UA [auth u] Focus chain V Focus chain W Focus chain WA [auth w] Focus chain XA [auth x] Focus chain Y Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	GA [auth g], R, VA [auth v]	6		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain R Focus chain VA [auth v] Interactions & Density Focus chain GA [auth g] Focus chain R Focus chain VA [auth v]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 10
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	BB [auth 1], MA [auth m], X	4		N-Glycosylation	Interactions Focus chain BB [auth 1] Focus chain MA [auth m] Focus chain X Interactions & Density Focus chain BB [auth 1] Focus chain MA [auth m] Focus chain X
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 TB [auth I] SDF format, chain SB [auth I] SDF format, chain RB [auth I] SDF format, chain QB [auth F] SDF format, chain PB [auth F] SDF format, chain OB [auth C] SDF format, chain NB [auth C] SDF format, chain MB [auth C] SDF format, chain LB [auth A] SDF format, chain KB [auth A] SDF format, chain JB [auth G] SDF format, chain IB [auth G] SDF format, chain HB [auth G] SDF format, chain GB [auth B] SDF format, chain FB [auth B] MOL2 format, chain TB [auth I] MOL2 format, chain SB [auth I] MOL2 format, chain RB [auth I] MOL2 format, chain QB [auth F] MOL2 format, chain PB [auth F] MOL2 format, chain OB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain LB [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain JB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain GB [auth B] MOL2 format, chain FB [auth B] mmCIF format, chain TB [auth I] mmCIF format, chain SB [auth I] mmCIF format, chain RB [auth I] mmCIF format, chain QB [auth F] mmCIF format, chain PB [auth F] mmCIF format, chain OB [auth C] mmCIF format, chain NB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain LB [auth A] mmCIF format, chain KB [auth A] mmCIF format, chain JB [auth G] mmCIF format, chain IB [auth G] mmCIF format, chain HB [auth G] mmCIF format, chain GB [auth B] mmCIF format, chain FB [auth B]	FB [auth B] GB [auth B] HB [auth G] IB [auth G] JB [auth G] FB [auth B], GB [auth B], HB [auth G], IB [auth G], JB [auth G], KB [auth A], LB [auth A], MB [auth C], NB [auth C], OB [auth C], PB [auth F], QB [auth F], RB [auth I], SB [auth I], TB [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain KB [auth A] Focus chain LB [auth A] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth I] Focus chain SB [auth I] Focus chain TB [auth I] Interactions & Density Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain KB [auth A] Focus chain LB [auth A] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth I] Focus chain SB [auth I] Focus chain TB [auth I]