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- PDB-8zsb: Cryo-EM structure of human ZnT1, in the absence of zinc, determin... -

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Basic information

Entry
Database: PDB / ID: 8zsb
TitleCryo-EM structure of human ZnT1, in the absence of zinc, determined in outward-facing conformation
ComponentsProton-coupled zinc antiporter SLC30A1
KeywordsTRANSPORT PROTEIN / Copper uptake / Cuproptosis / ZnT family
Function / homology
Function and homology information


negative regulation of zinc ion transmembrane import / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion transmembrane transporter activity / zinc ion transport ...negative regulation of zinc ion transmembrane import / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / negative regulation of calcium ion import / negative regulation of neurotransmitter secretion / intracellular zinc ion homeostasis / calcium ion import / calcium channel inhibitor activity / T-tubule / postsynaptic density membrane / cytoplasmic vesicle membrane / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / basolateral plasma membrane / nuclear membrane / in utero embryonic development / defense response to bacterium / Golgi apparatus / endoplasmic reticulum / 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: 3.26 Å
AuthorsMa, J. / Zheng, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: to be published
Title: Zinc transporter 1 functions in copper uptake and cuproptosis
Authors: Li, Y. / Ma, J. / Wang, R. / Luo, Y. / Zheng, S. / Wang, X.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)110,8564
Polymers110,7252
Non-polymers1312
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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Cryo-EM structure of the ZnT1 in the apo state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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 magnification: 64000 X / Nominal defocus max: 3250 nm / Nominal defocus min: 1230 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 890

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 709780 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024892
ELECTRON MICROSCOPYf_angle_d0.5176651
ELECTRON MICROSCOPYf_dihedral_angle_d4.295650
ELECTRON MICROSCOPYf_chiral_restr0.041797
ELECTRON MICROSCOPYf_plane_restr0.005830

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