8ZP2 | pdb_00008zp2

Cryo-EM structure of human norepinephrine transporter NET bound with atomoxetine in an outward-open state at a resolution of 2.4 angstrom

PDB DOI: https://doi.org/10.2210/pdb8ZP2/pdb
EM Map EMD-60325: EMDB EMDataResource

Classification: TRANSPORT PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2024-05-29 Released: 2024-09-11
Deposition Author(s): Song, A.L., Wu, X.D.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Mechanistic insights of substrate transport and inhibitor binding revealed by high-resolution structures of human norepinephrine transporter.

Song, A., Wu, X.

(2024) Cell Res 34: 810-813

PubMed: 39223283 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-024-01024-0
Primary Citation Related Structures:
8ZOY, 8ZP1, 8ZP2, 8ZPB

Organizational Affiliation

Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.

Macromolecule Content

Total Structure Weight: 78.71 kDa
Atom Count: 5,504
Modeled Residue Count: 674
Deposited Residue Count: 691
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent noradrenaline transporter	A	571	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb_BB4	B	120	Lama glama	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY (Subject of Investigation/LOI) Query on PTY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
A1LX4 (Subject of Investigation/LOI) Query on A1LX4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine C₁₇ H₂₁ N O VHGCDTVCOLNTBX-QGZVFWFLSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Song, A.L.

Wu, X.D.

Funding Organization	Location	Grant Number
Other private	China	--

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-09-18
Changes: Data collection, Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary
Version 1.3: 2025-07-23
Changes: Data collection