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- PDB-9kzw: structure of hZnT1 in apo state -

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Basic information

Entry
Database: PDB / ID: 9kzw
Titlestructure of hZnT1 in apo state
ComponentsProton-coupled zinc antiporter SLC30A1
KeywordsTRANSPORT PROTEIN / transporter / Zn / cancer / drug target
Function / homology
Function and homology information


negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / cadmium ion transmembrane transport / negative regulation of calcium ion import ...negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / cadmium ion transmembrane transport / negative regulation of calcium ion import / regulation of postsynaptic density protein 95 clustering / zinc ion transport / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / negative regulation of neurotransmitter secretion / positive regulation of dendritic spine morphogenesis / intracellular zinc ion homeostasis / calcium ion import / postsynaptic density, intracellular component / calcium channel inhibitor activity / T-tubule / cytoplasmic vesicle membrane / postsynaptic density membrane / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / nuclear membrane / basolateral plasma membrane / in utero embryonic development / defense response to bacterium / Golgi membrane / dendrite / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain
Similarity search - Domain/homology
Proton-coupled zinc antiporter SLC30A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsXu, B. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908500 China
CitationJournal: Protein Cell / Year: 2025
Title: Bardoxolone methyl blocks the efflux of Zn2+ by targeting hZnT1 to inhibit the proliferation and metastasis of cervical cancer.
Authors: Yaxin Wang / Qinqin Liang / Shengjian Liang / Yuanyue Shan / Sai Shi / Xiaoyu Zhou / Ziyu Wang / Zhili Xu / Duanqing Pei / Mingfeng Zhang / Zhiyong Lou / Binghong Xu / Sheng Ye /
History
DepositionDec 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton-coupled zinc antiporter SLC30A1
B: Proton-coupled zinc antiporter SLC30A1


Theoretical massNumber of molelcules
Total (without water)110,7252
Polymers110,7252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Proton-coupled zinc antiporter SLC30A1 / Solute carrier family 30 member 1 / Zinc transporter 1


Mass: 55362.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A1, ZNT1 / Production host: Homo sapiens (human) / References: UniProt: Q9Y6M5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hZnT1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 568835 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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