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- PDB-6c5r: Crystal structure of the soluble domain of the mitochondrial calc... -

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Basic information

Entry
Database: PDB / ID: 6c5r
TitleCrystal structure of the soluble domain of the mitochondrial calcium uniporter
Componentscalcium uniporter
KeywordsCYTOSOLIC PROTEIN
Function / homologyuniporter activity / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / mitochondrial calcium ion homeostasis / calcium channel activity / mitochondrial inner membrane / identical protein binding / Calcium uniporter protein
Function and homology information
Biological speciesMetarhizium acridum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.09608311048 Å
AuthorsFan, C. / Fan, M. / Fastman, N. / Zhang, J. / Feng, L.
CitationJournal: Nature / Year: 2018
Title: X-ray and cryo-EM structures of the mitochondrial calcium uniporter.
Authors: Chao Fan / Minrui Fan / Benjamin J Orlando / Nathan M Fastman / Jinru Zhang / Yan Xu / Melissa G Chambers / Xiaofang Xu / Kay Perry / Maofu Liao / Liang Feng /
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 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.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: calcium uniporter
B: calcium uniporter
D: calcium uniporter
F: calcium uniporter
H: calcium uniporter
C: calcium uniporter
E: calcium uniporter
G: calcium uniporter


Theoretical massNumber of molelcules
Total (without water)194,1418
Polymers194,1418
Non-polymers00
Water0
1
A: calcium uniporter
B: calcium uniporter
H: calcium uniporter
G: calcium uniporter


Theoretical massNumber of molelcules
Total (without water)97,0714
Polymers97,0714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-80 kcal/mol
Surface area34970 Å2
MethodPISA
2
D: calcium uniporter
F: calcium uniporter
C: calcium uniporter
E: calcium uniporter


Theoretical massNumber of molelcules
Total (without water)97,0714
Polymers97,0714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-76 kcal/mol
Surface area36600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.785, 119.921, 88.005
Angle α, β, γ (deg.)90.000, 106.887, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
calcium uniporter


Mass: 24267.676 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metarhizium acridum (strain CQMa 102) (fungus)
Strain: CQMa 102 / Gene: MAC_01752 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: E9DVV4

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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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M glycine, pH 9.3, 15.5% PEG 4000, and 0.6 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09608311048→50 Å / Num. obs: 47337 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 97.3071351599 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.1
Reflection shellResolution: 3.1→3.17 Å / Num. unique obs: 3153

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 3.09608311048→42.105090976 Å / SU ML: 0.448428869909 / Cross valid method: FREE R-VALUE / σ(F): 1.33787117744 / Phase error: 34.267652959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.306400346901 2006 4.24155283968 %
Rwork0.261899995368 45288 -
obs0.263784373481 47294 99.4553445629 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.0706387757 Å2
Refinement stepCycle: LAST / Resolution: 3.09608311048→42.105090976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9966 0 0 0 9966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033520155158510173
X-RAY DIFFRACTIONf_angle_d0.66007774019413759
X-RAY DIFFRACTIONf_chiral_restr0.04289025374541534
X-RAY DIFFRACTIONf_plane_restr0.005115498047411751
X-RAY DIFFRACTIONf_dihedral_angle_d7.635566565716180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0961-3.17350.3953846292591430.3818206508493032X-RAY DIFFRACTION93.8238770686
3.1735-3.25930.3499480953911390.3713265727013253X-RAY DIFFRACTION99.8822143698
3.2593-3.35510.4032021108081460.3620978899143239X-RAY DIFFRACTION99.9409506938
3.3551-3.46340.366416433031300.3280184269293208X-RAY DIFFRACTION99.9700509134
3.4634-3.58710.3452816646521560.3086010586823227X-RAY DIFFRACTION99.9704491726
3.5871-3.73060.3212794686751410.3063175789483237X-RAY DIFFRACTION99.9408284024
3.7306-3.90030.3258588170111400.2920212236083254X-RAY DIFFRACTION99.8822836963
3.9003-4.10580.3319214628111480.2724020895573249X-RAY DIFFRACTION100
4.1058-4.36280.2772355728911440.2379419643643249X-RAY DIFFRACTION99.9705362404
4.3628-4.69920.3283572945581440.2333675766013221X-RAY DIFFRACTION100
4.6992-5.17130.2953898640891440.2295983914183279X-RAY DIFFRACTION99.9416058394
5.1713-5.91790.2944844893511410.2373268443493261X-RAY DIFFRACTION99.8532433226
5.9179-7.44920.3020323368081460.2568805939313262X-RAY DIFFRACTION99.7950219619
7.4492-42.1090.2579193646691440.2335058670913317X-RAY DIFFRACTION99.4540229885

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