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- EMDB-22286: Cryo-EM structure of human ZnT8 WT, in the presence of zinc, dete... -

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Entry
Database: EMDB / ID: EMD-22286
TitleCryo-EM structure of human ZnT8 WT, in the presence of zinc, determined in outward-facing conformation
Map dataCryo-EM structure of human ZnT8 WT, in the presence of zinc, determined in outward-facing conformation
Sample
  • Complex: Human Znt8 WT in the presence of zinc
    • Protein or peptide: Zinc transporter 8
  • Ligand: ZINC ION
KeywordsZnT8 / zinc transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


zinc ion import across plasma membrane / Zinc efflux and compartmentalization by the SLC30 family / insulin processing / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / regulation of vesicle-mediated transport / intracellular zinc ion homeostasis ...zinc ion import across plasma membrane / Zinc efflux and compartmentalization by the SLC30 family / insulin processing / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / regulation of vesicle-mediated transport / intracellular zinc ion homeostasis / insulin secretion / response to zinc ion / transport vesicle membrane / Insulin processing / response to type II interferon / response to glucose / response to interleukin-1 / secretory granule membrane / secretory granule / positive regulation of insulin secretion / cytoplasmic vesicle / Golgi membrane / intracellular membrane-bounded organelle / protein homodimerization activity / zinc ion binding / plasma membrane
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 SLC30A8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBai XC / Xue J
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations.
Authors: Jing Xue / Tian Xie / Weizhong Zeng / Youxing Jiang / Xiao-Chen Bai /
Abstract: ZnT8 is a Zn/H antiporter that belongs to SLC30 family and plays an essential role in regulating Zn accumulation in the insulin secretory granules of pancreatic β cells. However, the Zn/H exchange ...ZnT8 is a Zn/H antiporter that belongs to SLC30 family and plays an essential role in regulating Zn accumulation in the insulin secretory granules of pancreatic β cells. However, the Zn/H exchange mechanism of ZnT8 remains unclear due to the lack of high-resolution structures. Here, we report the cryo-EM structures of human ZnT8 (HsZnT8) in both outward- and inward-facing conformations. HsZnT8 forms a dimeric structure with four Zn binding sites within each subunit: a highly conserved primary site in transmembrane domain (TMD) housing the Zn substrate; an interfacial site between TMD and C-terminal domain (CTD) that modulates the Zn transport activity of HsZnT8; and two adjacent sites buried in the cytosolic domain and chelated by conserved residues from CTD and the His-Cys-His (HCH) motif from the N-terminal segment of the neighboring subunit. A comparison of the outward- and inward-facing structures reveals that the TMD of each HsZnT8 subunit undergoes a large structural rearrangement, allowing for alternating access to the primary Zn site during the transport cycle. Collectively, our studies provide the structural insights into the Zn/H exchange mechanism of HsZnT8.
History
DepositionJul 8, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xpe
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22286.png

Downloads & links

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Map

FileDownload / File: emd_22286.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human ZnT8 WT, in the presence of zinc, determined in outward-facing conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 200 pix.
= 166. Å		0.83 Å/pix.
x 200 pix.
= 166. Å		0.83 Å/pix.
x 200 pix.
= 166. 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: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.019755958 - 0.046138734
Average (Standard dev.)0.0007205462 (±0.0028168308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 166.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z166.000166.000166.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0200.0460.001

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Supplemental data

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Sample components

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Entire : Human Znt8 WT in the presence of zinc

EntireName: Human Znt8 WT in the presence of zinc
Components
  • Complex: Human Znt8 WT in the presence of zinc
    • Protein or peptide: Zinc transporter 8
  • Ligand: ZINC ION

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Supramolecule #1: Human Znt8 WT in the presence of zinc

SupramoleculeName: Human Znt8 WT in the presence of zinc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Location in cell: Insulin secretory granule
Molecular weightTheoretical: 35 KDa

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Macromolecule #1: Zinc transporter 8

MacromoleculeName: Zinc transporter 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.088129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYHCHSGSKP TEKGANEYAY AKWKLCSASA ICFIFMIAEV VGGHIAGSLA VVTDAAHLLI DLTSFLLSLF SLWLSSKPPS KRLTFGWHR AEILGALLSI LCIWVVTGVL VYLACERLLY PDYQIQATVM IIVSSCAVAA NIVLTVVLHQ RCLGHNHKEV Q ANASVRAA ...String:
MYHCHSGSKP TEKGANEYAY AKWKLCSASA ICFIFMIAEV VGGHIAGSLA VVTDAAHLLI DLTSFLLSLF SLWLSSKPPS KRLTFGWHR AEILGALLSI LCIWVVTGVL VYLACERLLY PDYQIQATVM IIVSSCAVAA NIVLTVVLHQ RCLGHNHKEV Q ANASVRAA FVHALGDLFQ SISVLISALI IYFKPEYKIA DPICTFIFSI LVLASTITIL KDFSILLMEG VPKSLNYSGV KE LILAVDG VLSVHSLHIW SLTMNQVILS AHVATAASRD SQVVRREIAK ALSKSFTMHS LTIQMESPVD QDPDCLFCED PCD

UniProtKB: Proton-coupled zinc antiporter SLC30A8

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration4 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 419917
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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