9PS1 | pdb_00009ps1

Cryo-EM structure of NCLX with calcium (class 3a)

• PDB DOI: https://doi.org/10.2210/pdb9PS1/pdb
• EM Map EMD-71819: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-24 Released: 2025-09-10 
• Deposition Author(s): Zhang, J., Feng, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), The G. Harold and Leila Y. Mathers Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and mechanism of the mitochondrial calcium transporter NCLX.

Fan, M., Tsai, C.W., Zhang, J., Zhang, J., Krishnan, A.R., Liu, T.Y., Huang, Y.L., Aydin, D., Du, S., Sobecks, B.L., Rodriguez, M.X., Reiter, A.H., Bertozzi, C.R., Dror, R.O., Tsai, M.F., Feng, L.

(2025) Nature 646: 1272-1280

• PubMed: 40931067 
• DOI: https://doi.org/10.1038/s41586-025-09491-0
• Primary Citation of Related Structures:  
  9PS1, 9PS2, 9PS3, 9PS4, 9PS6, 9PS8


• PubMed Abstract: 
  

  As a key mitochondrial Ca ²⁺ transporter, NCLX regulates intracellular Ca ²⁺ signalling and vital mitochondrial processes ^1-3 . The importance of NCLX in cardiac and nervous-system physiology is reflected by acute heart failure and neurodegenerative disorders caused by its malfunction ^4-9 . Despite substantial advances in the field, the transport mechanisms of NCLX remain unclear. Here we report the cryo-electron microscopy structures of NCLX, revealing its architecture, assembly, major conformational states and a previously undescribed mechanism for alternating access. Functional analyses further reveal an unexpected transport function of NCLX as a H ⁺ /Ca ²⁺ exchanger, rather than as a Na ⁺ /Ca ²⁺ exchanger as widely believed ¹ . These findings provide critical insights into mitochondrial Ca ²⁺ homeostasis and signalling, offering clues for developing therapies to treat diseases related to abnormal mitochondrial Ca ²⁺ .

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. [e-mail].
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. [e-mail].
Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Department of Biology, Stanford University, Stanford, CA, USA.
Stanford Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. [e-mail].
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 192.23 kDa 
• Atom Count: 11,325 
• Modeled Residue Count: 1,464 
• Deposited Residue Count: 1,755 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NCLX	A [auth B], B [auth C], C [auth A]	585	Rattus norvegicus	Mutation(s): 0  Gene Names: Slc8b1, Nckx6, Nclx, Slc24a6
UniProt
Find proteins for Q6AXS0 (Rattus norvegicus) Explore Q6AXS0  Go to UniProtKB:  Q6AXS0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth B], E [auth C], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Zhang, J., Feng, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
The G. Harold and Leila Y. Mathers Foundation	United States	--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Data collection, Database references
• Version 1.2: 2025-11-05
  Changes: Data collection, Database references