6C5W | pdb_00006c5w

Crystal structure of the mitochondrial calcium uniporter

• PDB DOI: https://doi.org/10.2210/pdb6C5W/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Metarhizium acridum CQMa 102, unidentified
• Expression System: Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-01-17 Released: 2018-07-11 
• Deposition Author(s): Fan, C., Fan, M., Fastman, N., Zhang, J., Feng, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.299 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Literature

X-ray and cryo-EM structures of the mitochondrial calcium uniporter.

Fan, C., Fan, M., Orlando, B.J., Fastman, N.M., Zhang, J., Xu, Y., Chambers, M.G., Xu, X., Perry, K., Liao, M., Feng, L.

(2018) Nature 559: 575-579

• PubMed: 29995856 
• DOI: https://doi.org/10.1038/s41586-018-0330-9
• Primary Citation Related Structures: 
  6C5R, 6C5W


• PubMed Abstract: 
  

  Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU). Here, we determined the structures of the pore-forming MCU proteins from two fungi by X-ray crystallography and single-particle cryo-electron microscopy. The stoichiometry, overall architecture, and individual subunit structure differed markedly from those described in the recent nuclear magnetic resonance structure of Caenorhabditis elegans MCU. We observed a dimer-of-dimer architecture across species and chemical environments, which was corroborated by biochemical experiments. Structural analyses and functional characterization uncovered the roles of key residues in the pore. These results reveal a new ion channel architecture, provide insights into calcium coordination, selectivity and conduction, and establish a structural framework for understanding the mechanism of mitochondrial calcium uniporter function.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA.
Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
NE-CAT and Dept. of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Biophysics Program, Stanford University, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.53 kDa 
• Atom Count: 5,745 
• Modeled Residue Count: 736 
• Deposited Residue Count: 858 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calcium uniporter	A, B	312	Metarhizium acridum CQMa 102	Mutation(s): 0  Gene Names: MAC_01752 Membrane Entity: Yes
UniProt
Find proteins for E9DVV4 (Metarhizium acridum (strain CQMa 102)) Explore E9DVV4  Go to UniProtKB:  E9DVV4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	C, D [auth E]	117	unidentified	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.299 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.02	α = 90
b = 290.45	β = 90
c = 126.12	γ = 90

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Fan, C., Fan, M., Fastman, N., Zhang, J., Feng, L.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2018-07-25
  Changes: Data collection, Database references
• Version 1.2: 2018-08-08
  Changes: Data collection, Database references
• Version 1.3: 2018-10-03
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2019-04-24
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary