4N5X

Crystal structure of N-terminal calmodulin-like Calcium sensor of human mitochondrial ATP-Mg/Pi carrier SCaMC1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A Self-Sequestered Calmodulin-like Ca(2+) Sensor of Mitochondrial SCaMC Carrier and Its Implication to Ca(2+)-Dependent ATP-Mg/Pi Transport.

Yang, Q., Bruschweiler, S., Chou, J.J.

(2014) Structure 22: 209-217

  • DOI: 10.1016/j.str.2013.10.018
  • Primary Citation of Related Structures:  
    4N5X

  • PubMed Abstract: 

    • The mitochondrial carriers play essential roles in energy metabolism. The short Ca²⁺-binding mitochondrial carrier (SCaMC) transports ATP-Mg in exchange for Pi and is important for activities that depend on adenine nucleotides. SCaMC adopts, in addition to the transmembrane domain (TMD) that transports solutes, an extramembrane N-terminal domain (NTD) that regulates solute transport in a Ca²⁺-dependent manner ...

    The mitochondrial carriers play essential roles in energy metabolism. The short Ca²⁺-binding mitochondrial carrier (SCaMC) transports ATP-Mg in exchange for Pi and is important for activities that depend on adenine nucleotides. SCaMC adopts, in addition to the transmembrane domain (TMD) that transports solutes, an extramembrane N-terminal domain (NTD) that regulates solute transport in a Ca²⁺-dependent manner. Crystal structure of the Ca²⁺-bound NTD reveals a compact architecture in which the functional EF hands are sequestered by an endogenous helical segment. Nuclear magnetic resonance (NMR) relaxation rates indicated that removal of Ca²⁺ from NTD results in a major conformational switch from the rigid and compact Ca²⁺-bound state to the dynamic and loose apo state. Finally, we showed using surface plasmon resonance and NMR titration experiments that free apo NTDs could specifically interact with liposome-incorporated TMD, but that Ca²⁺ binding drastically weakened the interaction. Our results together provide a molecular explanation for Ca²⁺-dependent ATP-Mg flux in mitochondria.

    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: chou@cmcd.hms.harvard.edu.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calcium-binding mitochondrial carrier protein SCaMC-1A199Homo sapiensMutation(s): 1 
Gene Names: SLC25A24, APC1, MCSC1, SCAMC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NUK1 (Homo sapiens)
Explore Q6NUK1 
Go to UniProtKB:  Q6NUK1
PHAROS:  Q6NUK1
GTEx:  ENSG00000085491
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.21α = 90
b = 51.21β = 90
c = 112.153γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2018-06-13
    Changes: Data collection