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- PDB-8zb0: Cryo-EM structure of human ZnT1 -

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Basic information

Entry
Database: PDB / ID: 8zb0
TitleCryo-EM structure of human ZnT1
ComponentsProton-coupled zinc antiporter SLC30A1
KeywordsPROTEIN TRANSPORT / Transport / ZnT1 / Homodimer / Zinc / MEMBRAIN PROTEIN
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 efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / zinc:proton antiporter activity / cadmium ion transmembrane transport / regulation of postsynaptic density protein 95 clustering ...negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / zinc:proton antiporter activity / cadmium ion transmembrane transport / regulation of postsynaptic density protein 95 clustering / zinc ion transport / negative regulation of calcium ion import / zinc ion transmembrane transporter activity / negative regulation of neurotransmitter secretion / zinc ion transmembrane transport / 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 / Golgi apparatus / endoplasmic reticulum / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
Proton-coupled zinc antiporter SLC30A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSun, S. / Xie, E. / Xu, S. / Ji, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci (Weinh) / Year: 2024
Title: The Intestinal Transporter SLC30A1 Plays a Critical Role in Regulating Systemic Zinc Homeostasis.
Authors: Shumin Sun / Enjun Xie / Shan Xu / Suyu Ji / Shufen Wang / Jie Shen / Rong Wang / Xinyi Shen / Yunxing Su / Zijun Song / Xiaotian Wu / Jiahui Zhou / Zhaoxian Cai / Xiaopeng Li / Yan Zhang / ...Authors: Shumin Sun / Enjun Xie / Shan Xu / Suyu Ji / Shufen Wang / Jie Shen / Rong Wang / Xinyi Shen / Yunxing Su / Zijun Song / Xiaotian Wu / Jiahui Zhou / Zhaoxian Cai / Xiaopeng Li / Yan Zhang / Junxia Min / Fudi Wang /
Abstract: The essential trace element, zinc, regulates virtually all aspects of cellular physiology, particularly cell proliferation and survival. Diverse families of metal transporters, metallothioneins, and ...The essential trace element, zinc, regulates virtually all aspects of cellular physiology, particularly cell proliferation and survival. Diverse families of metal transporters, metallothioneins, and metal-responsive transcriptional regulators are linked to zinc homeostasis. However, the mechanism underlying the regulation of systemic zinc homeostasis remains largely unknown. Here, it is reported that the intestinal transporter SLC30A1 plays an essential role in maintaining systemic zinc homeostasis. Using several lines of tissue-specific knockout mice, it is found that intestinal Slc30a1 plays a critical role in survival. Furthermore, lineage tracing reveals that Slc30a1 is localized to the basolateral membrane of intestinal epithelial cells (IECs). It is also found that Slc30a1 safeguards both intestinal barrier integrity and systemic zinc homeostasis. Finally, an integrative analysis of the cryo-EM structure and site-specific mutagenesis of human SLC30A1 are performed and a zinc transport mechanism of SLC30A1 unique within the SLC30A family, with His43 serving as a critical residue for zinc selectivity, is identified.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,24810
Polymers110,7252
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: ZnT1 homodimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2188560 / Symmetry type: POINT

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