[English] 日本語
Yorodumi
- EMDB-62605: Cryo-EM structure of SLC30A10 in the absence of Mn2+, determined ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62605
TitleCryo-EM structure of SLC30A10 in the absence of Mn2+, determined in inward-facing conformation
Map data
Sample
  • Complex: SLC30A10 dimer of inward-facing at APO state
    • Protein or peptide: Calcium/manganese antiporter SLC30A10
KeywordsManganese Transpoter / SLC30A10 / ZnT10 / TRANSPORT PROTEIN
Function / homology
Function and homology information


manganese ion export across plasma membrane / calcium:manganese antiporter activity / detoxification of zinc ion / zinc ion import into organelle / Metal ion SLC transporters / manganese ion transport / intracellular manganese ion homeostasis / manganese ion transmembrane transporter activity / zinc ion transmembrane transporter activity / zinc ion transmembrane transport ...manganese ion export across plasma membrane / calcium:manganese antiporter activity / detoxification of zinc ion / zinc ion import into organelle / Metal ion SLC transporters / manganese ion transport / intracellular manganese ion homeostasis / manganese ion transmembrane transporter activity / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / intracellular zinc ion homeostasis / cellular response to angiotensin / recycling endosome / epidermal growth factor receptor signaling pathway / recycling endosome membrane / early endosome membrane / early endosome / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
Calcium/manganese antiporter SLC30A10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYang H / Zhang JK / Shen X
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171216 China
Ministry of Science and Technology (MoST, China)STI2030-Major Projects 2022ZD0212600 China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanisms of SLC30A10-mediated manganese transport.
Authors: Xurui Shen / Jinlun Kylian Zhang / Peixin Sun / Huiwen Zhong / Rui He / Shiliang Wang / Xiaojun Guo / Hanting Yang /
Abstract: Manganese ion (Mn²⁺) is crucial for various physiological processes, yet excessive levels disrupt cellular homeostasis and impair the function of multiple organelles. The transporter SLC30A10 ...Manganese ion (Mn²⁺) is crucial for various physiological processes, yet excessive levels disrupt cellular homeostasis and impair the function of multiple organelles. The transporter SLC30A10 plays a pivotal role in Mn²⁺ homeostasis by exporting Mn²⁺ from cells, preventing toxic effects. Mutations in the SLC30A10 gene result in Mn²⁺ accumulation and lead to disorders such as hypermanganesemia with dystonia 1 (HMNDYT1). Despite its physiological significance, the structural basis underlying Mn²⁺ binding and the detailed transport mechanisms of SLC30A10 remain unknown. Here, we present diverse conformations of high-resolution cryo-electron microscopy (cryo-EM) structures that reveal a Mn²⁺-binding site in SLC30A10, setting it apart from other SLC30 family transporters. Furthermore, we show that the HMNDYT1-associated D40A mutation interrupts Mn²⁺ binding and transport, identifying D40 as a potential therapeutic target. These findings provide structural insights into Mn²⁺ transport mechanisms mediated by SLC30A10, advancing our understanding of Mn²⁺ binding and potential targets for future therapeutic exploration.
History
DepositionDec 5, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62605.png

Downloads & links

-
Map

FileDownload / File: emd_62605.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16016811 - 0.32937422
Average (Standard dev.)0.000052808224 (±0.007792108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_62605_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62605_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62605_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SLC30A10 dimer of inward-facing at APO state

EntireName: SLC30A10 dimer of inward-facing at APO state
Components
  • Complex: SLC30A10 dimer of inward-facing at APO state
    • Protein or peptide: Calcium/manganese antiporter SLC30A10

-
Supramolecule #1: SLC30A10 dimer of inward-facing at APO state

SupramoleculeName: SLC30A10 dimer of inward-facing at APO state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Calcium/manganese antiporter SLC30A10

MacromoleculeName: Calcium/manganese antiporter SLC30A10 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.740832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRYSGKTCR LLFMLVLTVA FFVAELVSGY LGNSIALLSD SFNMLSDLIS LCVGLSAGYI ARRPTRGFSA TYGYARAEVV GALSNAVFL TALCFTIFVE AVLRLARPER IDDPELVLIV GVLGLLVNVV GLLIFQDCAA WFACCLRGRS RRLQQRQQLA E GCVPGAFG ...String:
MGRYSGKTCR LLFMLVLTVA FFVAELVSGY LGNSIALLSD SFNMLSDLIS LCVGLSAGYI ARRPTRGFSA TYGYARAEVV GALSNAVFL TALCFTIFVE AVLRLARPER IDDPELVLIV GVLGLLVNVV GLLIFQDCAA WFACCLRGRS RRLQQRQQLA E GCVPGAFG GPQGAEDPRR AADPTAPGSD SAVTLRGTSV ERKREKGATV FANVAGDSFN TQNEPEDMMK KEKKSEALNI RG VLLHVMG DALGSVVVVI TAIIFYVLPL KSEDPCNWQC YIDPSLTVLM VIIILSSAFP LIKETAAILL QMVPKGVNME ELM SKLSAV PGISSVHEVH IWELVSGKII ATLHIKYPKD RGYQDASTKI REIFHHAGIH NVTIQFENVD LKEPLEQKDL LLLC NSPCI SKGCAKQLCC PPGALPLAHV NGCAEHNGGP SLDTYGSDGL SRRDAREVAI EVSLDSCLSD HGQSLNKTQE DQCYV NRTH F

UniProtKB: Calcium/manganese antiporter SLC30A10

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225307
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
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