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- PDB-8j2g: Human ZnT1-D47N/D255N mutant -

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Basic information

Entry
Database: PDB / ID: 8j2g
TitleHuman ZnT1-D47N/D255N mutant
ComponentsProton-coupled zinc antiporter SLC30A1
KeywordsTRANSPORT PROTEIN / zinc exporter
Function / homology
Function and homology information


negative regulation of zinc ion transmembrane import / zinc export across plasma membrane / detoxification of zinc ion / zinc ion import into organelle / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / zinc ion transmembrane transporter activity / zinc ion transport ...negative regulation of zinc ion transmembrane import / zinc export across plasma membrane / detoxification of zinc ion / zinc ion import into organelle / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / 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 / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / 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: 3.4 Å
AuthorsSun, L. / Liu, X. / Sun, C. / He, B.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509302 China
CitationJournal: To Be Published
Title: Structure of the human ZnT1-D47N/D255N double mutant
Authors: Sun, L. / Liu, X. / Sun, C. / He, B.
History
DepositionApr 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 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


Theoretical massNumber of molelcules
Total (without water)110,7212
Polymers110,7212
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
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: 55360.633 Da / Num. of mol.: 2 / Mutation: D47N,D255N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A1, ZNT1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y6M5

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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: Human ZnT1-D47N/D255N mutant homodimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pCAG
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
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: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.13_2998: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 550472 / Symmetry type: POINT

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