[English] 日本語
Yorodumi
- EMDB-61515: Cryo-EM structure of human ZnT3 under acidic conditions -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61515
TitleCryo-EM structure of human ZnT3 under acidic conditions
Map data
Sample
  • Complex: ZnT3
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A3
Keywordszinc transporter / membrane protein / 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 / synaptic vesicle membrane / late endosome membrane / late endosome / 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 transmembrane domain
Similarity search - Domain/homology
Probable proton-coupled zinc antiporter SLC30A3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsIshida H / Yo R / Zhnag Z / Shimizu T / Ohto U
Funding support Japan, 1 items
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, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61515.png

Downloads & links

-
Map

FileDownload / File: emd_61515.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. 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: 0.0428
Minimum - Maximum-0.11881974 - 0.21482779
Average (Standard dev.)-0.0005515029 (±0.0042483476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_61515_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61515_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ZnT3

EntireName: ZnT3
Components
  • Complex: ZnT3
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A3

-
Supramolecule #1: ZnT3

SupramoleculeName: ZnT3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Probable proton-coupled zinc antiporter SLC30A3

MacromoleculeName: Probable proton-coupled zinc antiporter SLC30A3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.927316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPSPAAGGL ETTRLVSPRD RGGAGGSLRL KSLFTEPSEP LPEESKPVEM PFHHCHRDPL PPPGLTPERL HARRQLYAAC AVCFVFMAG EVVGGYLAHS LAIMTDAAHL LADVGSMMGS LFSLWLSTRP ATRTMTFGWH RSETLGALAS VVSLWMVTGI L LYLAFVRL ...String:
MEPSPAAGGL ETTRLVSPRD RGGAGGSLRL KSLFTEPSEP LPEESKPVEM PFHHCHRDPL PPPGLTPERL HARRQLYAAC AVCFVFMAG EVVGGYLAHS LAIMTDAAHL LADVGSMMGS LFSLWLSTRP ATRTMTFGWH RSETLGALAS VVSLWMVTGI L LYLAFVRL LHSDYHIEGG AMLLTASIAV CANLLMAFVL HQAGPPHSHG SRGAEYAPLE EGPEEPLPLG NTSVRAAFVH VL GDLLQSF GVLAASILIY FKPQYKAADP ISTFLFSICA LGSTAPTLRD VLRILMEGTP RNVGFEPVRD TLLSVPGVRA THE LHLWAL TLTYHVASAH LAIDSTADPE AVLAEASSRL YSRFGFSSCT LQVEQYQPEM AQCLRCQEPP QAGSIEGRIV KDYK DDDDK

UniProtKB: Probable proton-coupled zinc antiporter SLC30A3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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