9KVX | pdb_00009kvx

Cryo-EM structure of SLC30A10 in Mn2+-bound state, determined in inward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/manganese antiporter SLC30A10A [auth B],
B [auth A]
485Homo sapiensMutation(s): 0 
Gene Names: SLC30A10ZNT10ZNT8
Membrane Entity: Yes 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 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