6DT0 | pdb_00006dt0

Cryo-EM structure of a mitochondrial calcium uniporter

• PDB DOI: https://doi.org/10.2210/pdb6DT0/pdb
• EM Map EMD-8911: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Neurospora crassa
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-06-14 Released: 2018-07-11 
• Deposition Author(s): Yoo, J., Wu, M., Yin, Y., Herzik, M.A.J., Lander, G.C., Lee, S.-Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a mitochondrial calcium uniporter.

Yoo, J., Wu, M., Yin, Y., Herzik Jr., M.A., Lander, G.C., Lee, S.Y.

(2018) Science 361: 506-511

• PubMed: 29954988 
• DOI: https://doi.org/10.1126/science.aar4056
• Primary Citation Related Structures: 
  6DT0


• PubMed Abstract: 
  

  Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary mediator for calcium uptake into the mitochondrial matrix. Here, we present the cryo-electron microscopy structure of the full-length MCU from Neurospora crassa to an overall resolution of ~3.7 angstroms. Our structure reveals a tetrameric architecture, with the soluble and transmembrane domains adopting different symmetric arrangements within the channel. The conserved W-D-Φ-Φ-E-P-V-T-Y sequence motif of MCU pore forms a selectivity filter comprising two acidic rings separated by one helical turn along the central axis of the channel pore. The structure combined with mutagenesis gives insight into the basis of calcium recognition.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. [e-mail] [e-mail].
Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, cross-linking

Macromolecule Content 

• Total Structure Weight: 211.83 kDa 
• Atom Count: 7,133 
• Modeled Residue Count: 944 
• Deposited Residue Count: 1,832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial calcium uniporter	A, B, C, D	458	Neurospora crassa	Mutation(s): 1  Gene Names: NCU08166 Membrane Entity: Yes
UniProt
Find proteins for Q7S4I4 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7S4I4  Go to UniProtKB:  Q7S4I4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Yoo, J., Wu, M., Yin, Y., Herzik, M.A.J., Lander, G.C., Lee, S.-Y.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2018-08-15
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations