9JKF | pdb_00009jkf

Asymmetric structure of cleaved HIV-1 Tri FPPR envelope glycoprotein trimer in amphipol-lipid nanodiscs (Tri FPPR.1)

PDB DOI: https://doi.org/10.2210/pdb9JKF/pdb
EM Map EMD-61553: EMDB EMDataResource

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

Deposited: 2024-09-16 Released: 2025-02-26
Deposition Author(s): Qi, Y., Zhang, S., Sodroski, J., Mao, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The membrane-proximal external region of human immunodeficiency virus (HIV-1) envelope glycoprotein trimers in A18-lipid nanodiscs.

Qi, Y., Zhang, S., Wang, K., Ding, H., Zhang, Z., Anang, S., Nguyen, H.T., Kappes, J.C., Sodroski, J., Mao, Y.

(2025) Commun Biol 8: 442-442

PubMed: 40089599 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-025-07852-z
Primary Citation of Related Structures:
9JKF, 9JKG

PubMed Abstract:
During human immunodeficiency virus (HIV-1) entry, the metastable pretriggered envelope glycoprotein (Env) trimer ((gp120/gp41) ₃) opens asymmetrically. We present cryo-EM structures of cleaved asymmetric Env trimers in amphipol-lipid nanodiscs. The gp41 membrane-proximal external region (MPER) could be traced in Env protomers that remained close to the nanodisc despite Env tilting. The MPER interacts with the gp120 C-termini and gp41 α9 helices at the base of the Env trimer. MPER conformation is coupled with the tilt angles of the α9 helices, the helicity of the gp41 heptad repeat (HR1 _N) regions, and the opening angles between the protomers of the asymmetric trimers. Our structural models explain the stabilizing effects of MPER integrity and Env proteolytic maturation on the pretriggered Env conformation. Superimposed on the asymmetry of the Env protomers, variation in the glycans at the trimer apex creates substantial structural heterogeneity in the V2 quaternary epitopes of difficult-to-elicit broadly neutralizing antibodies.

Organizational Affiliation

Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

Macromolecule Content

Total Structure Weight: 540.62 kDa
Atom Count: 18,127
Modeled Residue Count: 1,884
Deposited Residue Count: 4,332
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth B] B [auth C] C [auth D] D [auth E] E [auth A] A [auth B], B [auth C], C [auth D], D [auth E], E [auth A], F	722	Simian-Human immunodeficiency virus	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for G1JZH9 (Simian-Human immunodeficiency virus) Explore G1JZH9 Go to UniProtKB: G1JZH9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1JZH9
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth B] Focus chain B [auth C] Focus chain C [auth D] Focus chain D [auth E] Focus chain E [auth A] Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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], CA [auth c], DB [auth 3], FB [auth 5], AA [auth a], AB [auth 0], CA [auth c], DB [auth 3], FB [auth 5], G, GA [auth g], HA [auth h], HB [auth 7], J, K, KB [auth AA], L, LB [auth BA], M, MA [auth m], OA [auth o], OB [auth EA], P, Q, QA [auth q], R, RA [auth r], SA [auth s], SB [auth IA], V, WA [auth w], Z, ZA [auth z]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain DB [auth 3] Focus chain FB [auth 5] Focus chain G Focus chain GA [auth g] Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain J Focus chain K Focus chain KB [auth AA] Focus chain L Focus chain LB [auth BA] Focus chain M Focus chain MA [auth m] Focus chain OA [auth o] Focus chain OB [auth EA] Focus chain P Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain SA [auth s] Focus chain SB [auth IA] Focus chain V Focus chain WA [auth w] Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain DB [auth 3] Focus chain FB [auth 5] Focus chain G Focus chain GA [auth g] Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain J Focus chain K Focus chain KB [auth AA] Focus chain L Focus chain LB [auth BA] Focus chain M Focus chain MA [auth m] Focus chain OA [auth o] Focus chain OB [auth EA] Focus chain P Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain SA [auth s] Focus chain SB [auth IA] Focus chain V Focus chain WA [auth w] Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	BA [auth b], EA [auth e], EB [auth 4], FA [auth f], GB [auth 6], BA [auth b], EA [auth e], EB [auth 4], FA [auth f], GB [auth 6], H, I, KA [auth k], LA [auth l], N, NA [auth n], RB [auth HA], U, UB [auth KA], VB [auth LA], WB [auth MA]	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain GB [auth 6] Focus chain H Focus chain I Focus chain KA [auth k] Focus chain LA [auth l] Focus chain N Focus chain NA [auth n] Focus chain RB [auth HA] Focus chain U Focus chain UB [auth KA] Focus chain VB [auth LA] Focus chain WB [auth MA] Interactions & Density Focus chain BA [auth b] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain GB [auth 6] Focus chain H Focus chain I Focus chain KA [auth k] Focus chain LA [auth l] Focus chain N Focus chain NA [auth n] Focus chain RB [auth HA] Focus chain U Focus chain UB [auth KA] Focus chain VB [auth LA] Focus chain WB [auth MA]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	O	3		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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	S	6		N-Glycosylation	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	T	5		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

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	BB [auth 1], IA [auth i], JA [auth j], W	5		N-Glycosylation	Interactions Focus chain BB [auth 1] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain W Interactions & Density Focus chain BB [auth 1] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain W
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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)-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	NB [auth DA], UA [auth u], X	7		N-Glycosylation	Interactions Focus chain NB [auth DA] Focus chain UA [auth u] Focus chain X Interactions & Density Focus chain NB [auth DA] Focus chain UA [auth u] Focus chain X
Glycosylation Resources
GlyTouCan: G23799GS GlyCosmos: G23799GS GlyGen: G23799GS

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	CB [auth 2], JB [auth 9], MB [auth CA], PB [auth FA], QB [auth GA], CB [auth 2], JB [auth 9], MB [auth CA], PB [auth FA], QB [auth GA], VA [auth v], Y	4		N-Glycosylation	Interactions Focus chain CB [auth 2] Focus chain JB [auth 9] Focus chain MB [auth CA] Focus chain PB [auth FA] Focus chain QB [auth GA] Focus chain VA [auth v] Focus chain Y Interactions & Density Focus chain CB [auth 2] Focus chain JB [auth 9] Focus chain MB [auth CA] Focus chain PB [auth FA] Focus chain QB [auth GA] Focus chain VA [auth v] Focus chain Y
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], TB [auth JA], YA [auth y]	4		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain TB [auth JA] Focus chain YA [auth y] Interactions & Density Focus chain DA [auth d] Focus chain TB [auth JA] Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	PA [auth p]	8		N-Glycosylation	Interactions Focus chain PA [auth p] Interactions & Density Focus chain PA [auth p]
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 12
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	TA [auth t], XA [auth x]	4		N-Glycosylation	Interactions Focus chain TA [auth t] Focus chain XA [auth x] Interactions & Density Focus chain TA [auth t] Focus chain XA [auth x]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	IB [auth 8]	6		N-Glycosylation	Interactions Focus chain IB [auth 8] Interactions & Density Focus chain IB [auth 8]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
83G Query on 83G Download Ideal Coordinates CCD File SDF format, chain AC [auth E] SDF format, chain CC [auth A] SDF format, chain XB [auth C] MOL2 format, chain AC [auth E] MOL2 format, chain CC [auth A] MOL2 format, chain XB [auth C] mmCIF format, chain AC [auth E] mmCIF format, chain CC [auth A] mmCIF format, chain XB [auth C]	AC [auth E], CC [auth A], XB [auth C]	1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione C₂₂ H₂₂ N₄ O₄ OKGPFTLYBPQBIX-CQSZACIVSA-N		Interactions Focus chain AC [auth E] Focus chain CC [auth A] Focus chain XB [auth C] Interactions & Density Focus chain AC [auth E] Focus chain CC [auth A] Focus chain XB [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BC [auth E] SDF format, chain DC [auth A] SDF format, chain YB [auth C] SDF format, chain ZB [auth C] MOL2 format, chain BC [auth E] MOL2 format, chain DC [auth A] MOL2 format, chain YB [auth C] MOL2 format, chain ZB [auth C] mmCIF format, chain BC [auth E] mmCIF format, chain DC [auth A] mmCIF format, chain YB [auth C] mmCIF format, chain ZB [auth C]	BC [auth E], DC [auth A], YB [auth C], ZB [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BC [auth E] Focus chain DC [auth A] Focus chain YB [auth C] Focus chain ZB [auth C] Interactions & Density Focus chain BC [auth E] Focus chain DC [auth A] Focus chain YB [auth C] Focus chain ZB [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	12125401
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Al124982