9PQ3 | pdb_00009pq3

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

PDB DOI: https://doi.org/10.2210/pdb9PQ3/pdb
EM Map EMD-71782: 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: 3.94 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: 240.76 kDa
Atom Count: 15,684
Modeled Residue Count: 1,728
Deposited Residue Count: 1,866
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 459C-ALT RnS DS-SOSIP gp41	A, C [auth B], E [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C [auth B] Focus chain E [auth F]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 459C-ALT RnS DS-SOSIP gp120	B [auth C], D [auth G], F [auth I]	469	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 B [auth C] Focus chain D [auth G] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	AA [auth a], DA [auth d], G [auth D], H [auth E], IA [auth i], AA [auth a], DA [auth d], G [auth D], H [auth E], IA [auth i], KA [auth k], L, LA [auth l], O, PA [auth p], SA [auth s], T, V, W, XA [auth x]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain G [auth D] Focus chain H [auth E] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain O Focus chain PA [auth p] Focus chain SA [auth s] Focus chain T Focus chain V Focus chain W Focus chain XA [auth x] Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain G [auth D] Focus chain H [auth E] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain O Focus chain PA [auth p] Focus chain SA [auth s] Focus chain T Focus chain V Focus chain W Focus chain XA [auth x]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	EA [auth e], FA [auth f], GA [auth g], HA [auth h], I [auth H], EA [auth e], FA [auth f], GA [auth g], HA [auth h], I [auth H], JA [auth j], K, MA [auth m], OA [auth o], P, Q, R, S, TA [auth t], U, UA [auth u], VA [auth v], WA [auth w], X, YA [auth y], Z	3		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth H] Focus chain JA [auth j] Focus chain K Focus chain MA [auth m] Focus chain OA [auth o] Focus chain P Focus chain Q Focus chain R Focus chain S 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 X Focus chain YA [auth y] Focus chain Z Interactions & Density Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth H] Focus chain JA [auth j] Focus chain K Focus chain MA [auth m] Focus chain OA [auth o] Focus chain P Focus chain Q Focus chain R Focus chain S 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 X Focus chain YA [auth y] Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
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	J, NA [auth n], Y	6		N-Glycosylation	Interactions Focus chain J Focus chain NA [auth n] Focus chain Y Interactions & Density Focus chain J Focus chain NA [auth n] Focus chain Y
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 6
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	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: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	CA [auth c], N, RA [auth r]	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain N Focus chain RA [auth r] Interactions & Density Focus chain CA [auth c] Focus chain N Focus chain RA [auth r]
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 C] SDF format, chain DB [auth C] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain GB [auth G] SDF format, chain IB [auth G] SDF format, chain KB [auth F] SDF format, chain NB [auth I] SDF format, chain ZA [auth A] SDF format, chain MB [auth I] SDF format, chain LB [auth I] SDF format, chain JB [auth F] SDF format, chain HB [auth G] SDF format, chain CB [auth C] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain KB [auth F] MOL2 format, chain NB [auth I] MOL2 format, chain ZA [auth A] MOL2 format, chain MB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain JB [auth F] MOL2 format, chain HB [auth G] MOL2 format, chain CB [auth C] mmCIF format, chain AB [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain GB [auth G] mmCIF format, chain IB [auth G] mmCIF format, chain KB [auth F] mmCIF format, chain NB [auth I] mmCIF format, chain ZA [auth A] mmCIF format, chain MB [auth I] mmCIF format, chain LB [auth I] mmCIF format, chain JB [auth F] mmCIF format, chain HB [auth G] mmCIF format, chain CB [auth C]	AB [auth A] BB [auth C] CB [auth C] DB [auth C] EB [auth B] AB [auth A], BB [auth C], CB [auth C], DB [auth C], EB [auth B], FB [auth B], GB [auth G], HB [auth G], IB [auth G], JB [auth F], KB [auth F], LB [auth I], MB [auth I], NB [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 C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth I] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth I] Focus chain ZA [auth A]