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- PDB-5kui: Human mitochondrial calcium uniporter (residues 72-189) crystal s... -

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Basic information

Entry
Database: PDB / ID: 5kui
TitleHuman mitochondrial calcium uniporter (residues 72-189) crystal structure with calcium.
ComponentsCalcium uniporter protein, mitochondrial
KeywordsMETAL TRANSPORT / beta-grasp fold N-terminal domain residues 72-189 mitochondrial calcium uniporter
Function / homology
Function and homology information


mitochondrial calcium ion transmembrane transport / uniporter activity / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis ...mitochondrial calcium ion transmembrane transport / uniporter activity / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / protein complex oligomerization / calcium channel complex / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / glucose homeostasis / mitochondrial inner membrane / mitochondrion / identical protein binding
Similarity search - Function
Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
Calcium uniporter protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsMok, M.C.Y. / Lee, S.K. / Junop, M.S. / Stathopulos, P.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)05239 Canada
CitationJournal: Cell Chem Biol / Year: 2016
Title: Structural Insights into Mitochondrial Calcium Uniporter Regulation by Divalent Cations.
Authors: Lee, S.K. / Shanmughapriya, S. / Mok, M.C. / Dong, Z. / Tomar, D. / Carvalho, E. / Rajan, S. / Junop, M.S. / Madesh, M. / Stathopulos, P.B.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium uniporter protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)13,8811
Polymers13,8811
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.280, 51.280, 71.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Calcium uniporter protein, mitochondrial / Coiled-coil domain-containing protein 109A


Mass: 13880.736 Da / Num. of mol.: 1 / Fragment: unp residues 72-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NE86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, 10 % PEG 8000, 1.3 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→71.71 Å / Num. obs: 2858 / % possible obs: 100 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHENIXphasing
PHENIXmodel building
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KUE

5kue


Resolution: 2.701→37.756 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.72
RfactorNum. reflection% reflection
Rfree0.2995 282 9.94 %
Rwork0.2731 --
obs0.2804 2837 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.701→37.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 0 15 730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004727
X-RAY DIFFRACTIONf_angle_d0.62994
X-RAY DIFFRACTIONf_dihedral_angle_d14.313443
X-RAY DIFFRACTIONf_chiral_restr0.051122
X-RAY DIFFRACTIONf_plane_restr0.008130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7031-3.40150.32971360.28821287X-RAY DIFFRACTION87
3.4015-17.48430.30571400.26751262X-RAY DIFFRACTION85

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