9PQ2 | pdb_00009pq2

Cryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer

PDB DOI: https://doi.org/10.2210/pdb9PQ2/pdb
EM Map EMD-71781: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-07-22 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: 3.33 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: 249.4 kDa
Atom Count: 16,167
Modeled Residue Count: 1,758
Deposited Residue Count: 1,920
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
459C-WT RnS DS-SOSIP gp120	A [auth C], C [auth G], E [auth I]	487	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 20	Glycosylation Focus chain A [auth C] Focus chain C [auth G] Focus chain E [auth I]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
459C-WT RnS DS-SOSIP gp41	B [auth A], D [auth B], F	153	Human immunodeficiency virus 1	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], DB [auth 3], EB [auth 4], FA [auth f], G [auth D], AB [auth 0], DB [auth 3], EB [auth 4], FA [auth f], G [auth D], JA [auth j], MA [auth m], NA [auth n], O, OA [auth o], S, V, W, WA [auth w], X	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain G [auth D] Focus chain JA [auth j] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain S Focus chain V Focus chain W Focus chain WA [auth w] Focus chain X Interactions & Density Focus chain AB [auth 0] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain G [auth D] Focus chain JA [auth j] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain S Focus chain V Focus chain W Focus chain WA [auth w] Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	H [auth E], HA [auth h], PA [auth p], Q, Y, H [auth E], HA [auth h], PA [auth p], Q, Y, YA [auth y]	5		N-Glycosylation	Interactions Focus chain H [auth E] Focus chain HA [auth h] Focus chain PA [auth p] Focus chain Q Focus chain Y Focus chain YA [auth y] Interactions & Density Focus chain H [auth E] Focus chain HA [auth h] Focus chain PA [auth p] Focus chain Q Focus chain Y Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	AA [auth a], BA [auth b], BB [auth 1], CB [auth 2], DA [auth d], AA [auth a], BA [auth b], BB [auth 1], CB [auth 2], DA [auth d], GA [auth g], I [auth H], IA [auth i], J, K, KA [auth k], LA [auth l], M, P, QA [auth q], R, RA [auth r], SA [auth s], T, U, UA [auth u], XA [auth x], Z, ZA [auth z]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain I [auth H] Focus chain IA [auth i] Focus chain J Focus chain K Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M Focus chain P Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain SA [auth s] Focus chain T Focus chain U Focus chain UA [auth u] Focus chain XA [auth x] Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain I [auth H] Focus chain IA [auth i] Focus chain J Focus chain K Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M Focus chain P Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain SA [auth s] Focus chain T Focus chain U Focus chain UA [auth u] Focus chain XA [auth x] Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
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	CA [auth c], L, TA [auth t]	6		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain L Focus chain TA [auth t] Interactions & Density Focus chain CA [auth c] Focus chain L Focus chain TA [auth t]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 7
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	EA [auth e], N, VA [auth v]	4		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain N Focus chain VA [auth v] Interactions & Density Focus chain EA [auth e] Focus chain N Focus chain VA [auth v]
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 NB [auth I] SDF format, chain MB [auth I] SDF format, chain LB [auth I] SDF format, chain KB [auth G] SDF format, chain JB [auth G] SDF format, chain IB [auth G] SDF format, chain HB [auth C] SDF format, chain GB [auth C] SDF format, chain FB [auth C] MOL2 format, chain NB [auth I] MOL2 format, chain MB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain KB [auth G] MOL2 format, chain JB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain HB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain FB [auth C] mmCIF format, chain NB [auth I] mmCIF format, chain MB [auth I] mmCIF format, chain LB [auth I] mmCIF format, chain KB [auth G] mmCIF format, chain JB [auth G] mmCIF format, chain IB [auth G] mmCIF format, chain HB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain FB [auth C]	FB [auth C] GB [auth C] HB [auth C] IB [auth G] JB [auth G] FB [auth C], GB [auth C], HB [auth C], IB [auth G], JB [auth G], KB [auth G], LB [auth I], MB [auth I], NB [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain KB [auth G] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth I] Interactions & Density Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain KB [auth G] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth I]