[English] 日本語
Yorodumi
- EMDB-22287: Cryo-EM structure of human ZnT8 WT, in the absence of zinc, deter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22287
TitleCryo-EM structure of human ZnT8 WT, in the absence of zinc, determined in heterogeneous conformations- one subunit in an inward-facing and the other in an outward-facing conformation
Map dataCryo-EM structure of human ZnT8 WT, in the absence of zinc, determined in heterogeneous conformations- one subunit in an inward-facing and the other in an outward-facing conformation
Sample
  • Complex: Human ZnT8 WT in the absence 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: 5.9 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xpf
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22287.png

Downloads & links

-
Map

FileDownload / File: emd_22287.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human ZnT8 WT, in the absence of zinc, determined in heterogeneous conformations- one subunit in an inward-facing and the other in an outward-facing conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 180 pix.
= 149.4 Å		0.83 Å/pix.
x 180 pix.
= 149.4 Å		0.83 Å/pix.
x 180 pix.
= 149.4 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: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.010029678 - 0.025830971
Average (Standard dev.)0.00069729675 (±0.0025008712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 149.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z149.400149.400149.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0100.0260.001

-
Supplemental data

-
Sample components

-
Entire : Human ZnT8 WT in the absence of zinc

EntireName: Human ZnT8 WT in the absence of zinc
Components
  • Complex: Human ZnT8 WT in the absence of zinc
    • Protein or peptide: Zinc transporter 8
  • Ligand: ZINC ION

-
Supramolecule #1: Human ZnT8 WT in the absence of zinc

SupramoleculeName: Human ZnT8 WT in the absence 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

-
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

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 159793
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more