9KVY | pdb_00009kvy

Cryo-EM structure of SLC30A10, determined in asymmetric conformations-one subunit in an inward-facing Mn2+-bound and the other in an outward-facing Mn2+-unbound conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9KVY

This is version 1.0 of the entry. See complete history

Literature

Molecular mechanisms of SLC30A10-mediated manganese transport.

Shen, X.Zhang, J.K.Sun, P.Zhong, H.He, R.Wang, S.Guo, X.Yang, H.

(2025) Nat Commun 16: 8581-8581

  • DOI: https://doi.org/10.1038/s41467-025-63616-7
  • Primary Citation Related Structures: 
    9KVX, 9KVY, 9KVZ

  • PubMed 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 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.


  • Organizational Affiliation
    • Zhongshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Brain Function and Disorders, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China.

Macromolecule Content 

  • Total Structure Weight: 105.54 kDa 
  • Atom Count: 4,454 
  • Modeled Residue Count: 583 
  • Deposited Residue Count: 970 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calcium/manganese antiporter SLC30A10
A, B
485Homo sapiensMutation(s): 0 
Gene Names: SLC30A10ZNT10ZNT8
UniProt & NIH Common Fund Data Resources
Find proteins for Q6XR72 (Homo sapiens)
Explore Q6XR72 
Go to UniProtKB:  Q6XR72
PHAROS:  Q6XR72
GTEx:  ENSG00000196660 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XR72
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171216
Ministry of Science and Technology (MoST, China)ChinaSTI2030-Major Projects 2022ZD0212600

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release