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- PDB-9jj1: Cryo-EM structure of human ZnT3 -

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Basic information

Entry
Database: PDB / ID: 9jj1
TitleCryo-EM structure of human ZnT3
ComponentsProbable proton-coupled zinc antiporter SLC30A3
KeywordsMEMBRANE PROTEIN / zinc transporter / ZnT / antiporter
Function / homology
Function and homology information


zinc ion import into synaptic vesicle / positive regulation of transport / hippocampal mossy fiber / zinc ion import into lysosome / Zinc efflux and compartmentalization by the SLC30 family / microvesicle / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / antiporter activity / response to zinc ion ...zinc ion import into synaptic vesicle / positive regulation of transport / hippocampal mossy fiber / zinc ion import into lysosome / Zinc efflux and compartmentalization by the SLC30 family / microvesicle / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / antiporter activity / response to zinc ion / hippocampal mossy fiber to CA3 synapse / synaptic vesicle membrane / late endosome membrane / late endosome / synaptic vesicle / neuron projection / lysosomal membrane / glutamatergic synapse / 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
Lauryl Maltose Neopentyl Glycol / Probable proton-coupled zinc antiporter SLC30A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsIshida, H. / Yo, R. / Zhnag, Z. / Shimizu, T. / Ohto, U.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)20K16274 and 22K07131 (H.I.); 22K15046 and 24K09349 (Z.Z.); 19H00976, 22H05184, and 23H00366 (T.S.); and 19H03164 and 22H02556 [U.O.) Japan
CitationJournal: To Be Published
Title: Structural basis for the zinc transporters, ZnT3 and ZnT4
Authors: Ishida, H. / Yo, R. / Zhang, Z. / Shimizu, T. / Ohto, U.
History
DepositionSep 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 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: Probable proton-coupled zinc antiporter SLC30A3
B: Probable proton-coupled zinc antiporter SLC30A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25710
Polymers87,8552
Non-polymers2,4038
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 Probable proton-coupled zinc antiporter SLC30A3 / Solute carrier family 30 member 3 / Zinc transporter 3 / ZnT-3


Mass: 43927.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A3, ZNT3 / Cell line (production host): expi293F / Production host: Homo sapiens (human) / References: UniProt: Q99726
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H88O22
Has ligand of interestN
Has protein modificationN

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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: ZnT3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 68 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: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034960
ELECTRON MICROSCOPYf_angle_d0.4926764
ELECTRON MICROSCOPYf_dihedral_angle_d10.707702
ELECTRON MICROSCOPYf_chiral_restr0.035814
ELECTRON MICROSCOPYf_plane_restr0.004826

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