9L00 | pdb_00009l00

structure of hZnT1-CDDO-ME complex

PDB DOI: https://doi.org/10.2210/pdb9L00/pdb
EM Map EMD-62681: EMDB EMDataResource

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

Deposited: 2024-12-11 Released: 2025-09-24
Deposition Author(s): Xu, B., Wang, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.78 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

Bardoxolone methyl blocks the efflux of Zn2+ by targeting hZnT1 to inhibit the proliferation and metastasis of cervical cancer.

Wang, Y., Liang, Q., Liang, S., Shan, Y., Shi, S., Zhou, X., Wang, Z., Xu, Z., Pei, D., Zhang, M., Lou, Z., Xu, B., Ye, S.

(2025) Protein Cell 16: 991-996

PubMed: 40470835 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/procel/pwaf044
Primary Citation of Related Structures:
9KZW, 9L00

Organizational Affiliation

School of Life Sciences, State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin 300072, China.

Macromolecule Content

Total Structure Weight: 111.74 kDa
Atom Count: 4,854
Modeled Residue Count: 614
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton-coupled zinc antiporter SLC30A1	A, B	507	Homo sapiens	Mutation(s): 0 Gene Names: SLC30A1, ZNT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M5 (Homo sapiens) Explore Q9Y6M5 Go to UniProtKB: Q9Y6M5
PHAROS: Q9Y6M5 GTEx: ENSG00000170385
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6M5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EIM (Subject of Investigation/LOI) Query on A1EIM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	methyl (4aS,6aR,6bS,8aR,12aS,14aS,14bS}-11-cyano-2,2,6a,6b,9,9,12a-heptamethyl-10,14-bis(oxidanylidene)-1,3,4,5,6,7,8,8a,14a,14b-decahydropicene-4a-carboxylate C₃₂ H₄₃ N O₄ WPTTVJLTNAWYAO-IIHRHBSVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release
Version 1.1: 2026-01-07
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.