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- EMDB-62681: structure of hZnT1-CDDO-ME complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62681
Titlestructure of hZnT1-CDDO-ME complex
Map data
Sample
  • Complex: hZnT1-CDDO-ME
    • Protein or peptide: Proton-coupled zinc antiporter SLC30A1
  • Ligand: methyl (4aS,6aR,6bS,8aR,12aS,14aS,14bS}-11-cyano-2,2,6a,6b,9,9,12a-heptamethyl-10,14-bis(oxidanylidene)-1,3,4,5,6,7,8,8a,14a,14b-decahydropicene-4a-carboxylate
Keywordstransporter / Zn / cancer / drug target / TRANSPORT 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 / 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 / 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 / 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 / negative regulation of calcium ion import / regulation of postsynaptic density protein 95 clustering / zinc ion transport / 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 / 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 family
Similarity search - Domain/homology
Proton-coupled zinc antiporter SLC30A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsXu B / Wang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: structure of hZnT1-CDDO-ME complex
Authors: Xu B / Wang Y
History
DepositionDec 11, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62681.png

Downloads & links

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Map

FileDownload / File: emd_62681.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.67522746 - 1.146693
Average (Standard dev.)0.00030862613 (±0.015571725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62681_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62681_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hZnT1-CDDO-ME

EntireName: hZnT1-CDDO-ME
Components
  • Complex: hZnT1-CDDO-ME
    • Protein or peptide: Proton-coupled zinc antiporter SLC30A1
  • Ligand: methyl (4aS,6aR,6bS,8aR,12aS,14aS,14bS}-11-cyano-2,2,6a,6b,9,9,12a-heptamethyl-10,14-bis(oxidanylidene)-1,3,4,5,6,7,8,8a,14a,14b-decahydropicene-4a-carboxylate

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Supramolecule #1: hZnT1-CDDO-ME

SupramoleculeName: hZnT1-CDDO-ME / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Proton-coupled zinc antiporter SLC30A1

MacromoleculeName: Proton-coupled zinc antiporter SLC30A1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.362605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGCWGRNRGR LLCMLALTFM FMVLEVVVSR VTSSLAMLSD SFHMLSDVLA LVVALVAERF ARRTHATQKN TFGWIRAEVM GALVNAIFL TGLCFAILLE AIERFIEPHE MQQPLVVLGV GVAGLLVNVL GLCLFHHHSG FSQDSGHGHS HGGHGHGHGL P KGPRVKST ...String:
MGCWGRNRGR LLCMLALTFM FMVLEVVVSR VTSSLAMLSD SFHMLSDVLA LVVALVAERF ARRTHATQKN TFGWIRAEVM GALVNAIFL TGLCFAILLE AIERFIEPHE MQQPLVVLGV GVAGLLVNVL GLCLFHHHSG FSQDSGHGHS HGGHGHGHGL P KGPRVKST RPGSSDINVA PGEQGPDQEE TNTLVANTSN SNGLKLDPAD PENPRSGDTV EVQVNGNLVR EPDHMELEED RA GQLNMRG VFLHVLGDAL GSVIVVVNAL VFYFSWKGCS EGDFCVNPCF PDPCKAFVEI INSTHASVYE AGPCWVLYLD PTL CVVMVC ILLYTTYPLL KESALILLQT VPKQIDIRNL IKELRNVEGV EEVHELHVWQ LAGSRIIATA HIKCEDPTSY MEVA KTIKD VFHNHGIHAT TIQPEFASVG SKSSVVPCEL ACRTQCALKQ CCGTLPQAPS GKDAEKTPAV SISCLELSNN LEKKP RRTK AENIPAVVIE IKNMPNKQPE SSL

UniProtKB: Proton-coupled zinc antiporter SLC30A1

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Macromolecule #2: methyl (4aS,6aR,6bS,8aR,12aS,14aS,14bS}-11-cyano-2,2,6a,6b,9,9,12...

MacromoleculeName: methyl (4aS,6aR,6bS,8aR,12aS,14aS,14bS}-11-cyano-2,2,6a,6b,9,9,12a-heptamethyl-10,14-bis(oxidanylidene)-1,3,4,5,6,7,8,8a,14a,14b-decahydropicene-4a-carboxylate
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1EIM
Molecular weightTheoretical: 505.688 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9kzw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 350390
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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