9PNI | pdb_00009pni

Cryo-EM structure of J601-1B2 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer

PDB DOI: https://doi.org/10.2210/pdb9PNI/pdb
EM Map EMD-71766: 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.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.83 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: 386.9 kDa
Atom Count: 21,161
Modeled Residue Count: 2,442
Deposited Residue Count: 3,222
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, C [auth B], E [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 Focus chain C [auth B] Focus chain E [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 C], D [auth G], F [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 C] Focus chain D [auth G] Focus chain F [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
J601-1B2 heavy chain	G [auth H], I [auth J], K [auth D]	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
J601-1B2 light chain	H [auth L], J [auth K], L [auth E]	214	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
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	AB [auth 0], BB [auth 1], FA [auth f], GA [auth g], IA [auth i], AB [auth 0], BB [auth 1], FA [auth f], GA [auth g], IA [auth i], JA [auth j], KA [auth k], M, MA [auth m], NA [auth n], Q, R, TA [auth t], U, UA [auth u], VA [auth v], WA [auth w], XA [auth x], Y, YA [auth y], Z	3		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain M Focus chain MA [auth m] Focus chain NA [auth n] Focus chain Q Focus chain R Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain VA [auth v] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain Z Interactions & Density Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain M Focus chain MA [auth m] Focus chain NA [auth n] Focus chain Q Focus chain R Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain VA [auth v] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
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 b], N, PA [auth p]	5		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain N Focus chain PA [auth p] Interactions & Density Focus chain BA [auth b] Focus chain N Focus chain PA [auth p]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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], HA [auth h], O, AA [auth a], CA [auth c], DA [auth d], HA [auth h], O, OA [auth o], QA [auth q], RA [auth r], S, X	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain HA [auth h] Focus chain O Focus chain OA [auth o] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain HA [auth h] Focus chain O Focus chain OA [auth o] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
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	EA [auth e], P, SA [auth s]	6		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain P Focus chain SA [auth s] Interactions & Density Focus chain EA [auth e] Focus chain P Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CB [auth A] SDF format, chain DB [auth A] 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 JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth G] SDF format, chain OB [auth G] SDF format, chain PB [auth G] SDF format, chain RB [auth F] SDF format, chain SB [auth I] SDF format, chain TB [auth I] SDF format, chain VB [auth I] SDF format, chain WB [auth I] SDF format, chain QB [auth F] SDF format, chain IB [auth C] MOL2 format, chain CB [auth A] MOL2 format, chain DB [auth A] 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 JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth G] MOL2 format, chain OB [auth G] MOL2 format, chain PB [auth G] MOL2 format, chain RB [auth F] MOL2 format, chain SB [auth I] MOL2 format, chain TB [auth I] MOL2 format, chain VB [auth I] MOL2 format, chain WB [auth I] MOL2 format, chain QB [auth F] MOL2 format, chain IB [auth C] mmCIF format, chain CB [auth A] mmCIF format, chain DB [auth A] 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 JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth G] mmCIF format, chain OB [auth G] mmCIF format, chain PB [auth G] mmCIF format, chain RB [auth F] mmCIF format, chain SB [auth I] mmCIF format, chain TB [auth I] mmCIF format, chain VB [auth I] mmCIF format, chain WB [auth I] mmCIF format, chain QB [auth F] mmCIF format, chain IB [auth C]	CB [auth A] DB [auth A] EB [auth C] FB [auth C] GB [auth C] CB [auth A], DB [auth A], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth B], KB [auth B], LB [auth B], MB [auth G], OB [auth G], PB [auth G], QB [auth F], RB [auth F], SB [auth I], TB [auth I], VB [auth I], WB [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth A] Focus chain DB [auth A] 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 B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth G] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain VB [auth I] Focus chain WB [auth I] Interactions & Density Focus chain CB [auth A] Focus chain DB [auth A] 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 B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth G] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain VB [auth I] Focus chain WB [auth I]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain NB [auth G] SDF format, chain UB [auth I] MOL2 format, chain NB [auth G] MOL2 format, chain UB [auth I] mmCIF format, chain NB [auth G] mmCIF format, chain UB [auth I]	NB [auth G], UB [auth I]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain NB [auth G] Focus chain UB [auth I] Interactions & Density Focus chain NB [auth G] Focus chain UB [auth I]