9K6X | pdb_00009k6x

Structural and functional basis of antinociceptive action of conotoxin AoIA at the noradrenaline transporter

PDB DOI: https://doi.org/10.2210/pdb9K6X/pdb
EM Map EMD-62139: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Conus marmoreus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-10-22 Released: 2026-05-06
Deposition Author(s): Zhang, H., Harald, S., Oliver, B., Xu, E.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.77 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

Structural and functional basis of antinociceptive action of chi-conotoxin AoIA at the noradrenaline transporter.

Belleza, O.J.V., Zhang, H., Schmidhammer, H., Gonzalez, T.I., Ciotu, C.I., Tomasevic, N., Ocampo, C.M.M., Fernando, J.C., Koehbach, J., Schwarz, P., Al Makhlouf, M., Tajti, G., Hasinger, S., Kastner, N., Avsar, O., Retzl, B., Jantsch, K., Jiang, Y., Hellinger, R., Fischer, M.J.M., Rosengren, K.J., Gruber, C.W., Villaraza, A.J.L., Stockner, T., Spetea, M., Xu, H.E., Sitte, H.H.

(2026) Nat Struct Mol Biol

PubMed: 42481720 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-026-01838-z
Primary Citation Related Structures:
9K6X, 9PAZ, 9PB0

PubMed Abstract:
The χ-conotoxins are venom-derived peptides that specifically target the noradrenaline transporter (also known as norepinephrine transporter, NET). Regulation of noradrenergic signaling by NET affects neurophysiological processes, including pain. Therefore, the χ-conotoxin MrIA and its synthetic analogs have been previously investigated for their analgesic activity. Here we describe the synthesis and pharmacological characterization of χ-AoIA, a peptide that selectively inhibits NET with a higher potency compared to MrIA in in vitro radiotracer flux assays. Furthermore, we resolved the structure of the human NET:χ-AoIA complex by cryogenic electron microscopy, which revealed an atypical binding mode consisting of both the central binding site and the outer vestibule of the transporter. Lastly, χ-AoIA displays antinociceptive efficacy in a model of inflammatory pain after subcutaneous administration in mice. Our results demonstrate the efficacy of χ-AoIA as a highly selective ligand of NET and provide a mechanistic basis for its potential development as a nonopioid analgesic.

Organizational Affiliation

Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.

Macromolecule Content

Total Structure Weight: 150.66 kDa
Atom Count: 9,446
Modeled Residue Count: 1,122
Deposited Residue Count: 1,280
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conotoxin AoIA	A [auth C], D	11	Conus marmoreus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent noradrenaline transporter	B [auth A], C [auth B]	629	Homo sapiens	Mutation(s): 0 Gene Names: SLC6A2, NAT1, NET1, SLC6A5
UniProt & NIH Common Fund Data Resources
Find proteins for P23975 (Homo sapiens) Explore P23975 Go to UniProtKB: P23975
PHAROS: P23975 GTEx: ENSG00000103546
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23975
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EET (Subject of Investigation/LOI) Query on A1EET Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain S [auth B]	E [auth A], S [auth B]	[(2~{R})-3-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propyl] (9~{Z},12~{Z})-octadeca-9,12-dienoate C₂₄ H₄₅ O₉ P VEEHTGYBVMTAAF-RFFZIGDUSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain S [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth B], Q [auth B], R [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain V [auth B] MOL2 format, chain H [auth A] MOL2 format, chain V [auth B] mmCIF format, chain H [auth A] mmCIF format, chain V [auth B]	H [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain V [auth B] Interactions & Density Focus chain H [auth A] Focus chain V [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	F [auth A], G [auth A], T [auth B], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain T [auth B] Focus chain U [auth B]