4XTB | pdb_00004xtb

Crystal structure of the N-terminal domain of the human mitochondrial calcium uniporter

• PDB DOI: https://doi.org/10.2210/pdb4XTB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-23 Released: 2015-09-16 
• Deposition Author(s): Lee, Y., Min, C.K., Kim, T.G., Song, H.K., Lim, Y., Kim, D., Shin, K., Kang, M., Kang, J.Y., Youn, H.-S., Lee, J.-G., An, J.Y., Park, K.R., Lim, J.J., Kim, J.H., Kim, J.H., Park, Z.Y., Kim, Y.-S., Wang, J., Kim, D.H., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.176 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.140 (Depositor) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structure and function of the N-terminal domain of the human mitochondrial calcium uniporter.

Lee, Y., Min, C.K., Kim, T.G., Song, H.K., Lim, Y., Kim, D., Shin, K., Kang, M., Kang, J.Y., Youn, H.S., Lee, J.G., An, J.Y., Park, K.R., Lim, J.J., Kim, J.H., Kim, J.H., Park, Z.Y., Kim, Y.S., Wang, J., Kim, D.H., Eom, S.H.

(2015) EMBO Rep 16: 1318-1333

• PubMed: 26341627 
• DOI: https://doi.org/10.15252/embr.201540436
• Primary Citation Related Structures: 
  4XSJ, 4XTB, 5BZ6


• PubMed Abstract: 
  

  The mitochondrial calcium uniporter (MCU) is responsible for mitochondrial calcium uptake and homeostasis. It is also a target for the regulation of cellular anti-/pro-apoptosis and necrosis by several oncogenes and tumour suppressors. Herein, we report the crystal structure of the MCU N-terminal domain (NTD) at a resolution of 1.50 Å in a novel fold and the S92A MCU mutant at 2.75 Å resolution; the residue S92 is a predicted CaMKII phosphorylation site. The assembly of the mitochondrial calcium uniporter complex (uniplex) and the interaction with the MCU regulators such as the mitochondrial calcium uptake-1 and mitochondrial calcium uptake-2 proteins (MICU1 and MICU2) are not affected by the deletion of MCU NTD. However, the expression of the S92A mutant or a NTD deletion mutant failed to restore mitochondrial Ca(2+) uptake in a stable MCU knockdown HeLa cell line and exerted dominant-negative effects in the wild-type MCU-expressing cell line. These results suggest that the NTD of MCU is essential for the modulation of MCU function, although it does not affect the uniplex formation.

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Organizational Affiliation: 
• School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea.
School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea.
Graduate School of New Drug Discovery & Development, Chungnam National University, Daejon, Korea.
School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea.
Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea Department of Molecular Biochemistry and Biophysics, Yale University, New Haven, CT, USA.
School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea [e-mail] [e-mail].
School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.28 kDa 
• Atom Count: 1,030 
• Modeled Residue Count: 109 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uniporter protein, mitochondrial	A	123	Homo sapiens	Mutation(s): 0  Gene Names: MCU, C10orf42, CCDC109A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NE86 (Homo sapiens) Explore Q8NE86  Go to UniProtKB:  Q8NE86
PHAROS:  Q8NE86 GTEx:  ENSG00000156026

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.176 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.140 (Depositor) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.463	α = 90
b = 55.463	β = 90
c = 68.929	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Lee, Y., Min, C.K., Kim, T.G., Song, H.K., Lim, Y., Kim, D., Shin, K., Kang, M., Kang, J.Y., Youn, H.-S., Lee, J.-G., An, J.Y., Park, K.R., Lim, J.J., Kim, J.H., Kim, J.H., Park, Z.Y., Kim, Y.-S., Wang, J., Kim, D.H., Eom, S.H.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Other
• Version 1.2: 2015-10-14
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description