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- PDB-6c5w: Crystal structure of the mitochondrial calcium uniporter -

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Basic information

Entry
Database: PDB / ID: 6c5w
TitleCrystal structure of the mitochondrial calcium uniporter
Components
  • calcium uniporter
  • nanobodySingle-domain antibody
KeywordsMEMBRANE 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)
unknown (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.10010233314 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 17, 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 1.3Oct 3, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support

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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
C: nanobody
E: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5335
Polymers96,4934
Non-polymers401
Water0
1
A: calcium uniporter
E: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2873
Polymers48,2472
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: calcium uniporter
C: nanobody


Theoretical massNumber of molelcules
Total (without water)48,2472
Polymers48,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.020, 290.450, 126.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-501-

CA

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Components

#1: Protein calcium uniporter


Mass: 35555.496 Da / Num. of mol.: 2
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
#2: Antibody nanobody / Single-domain antibody


Mass: 12691.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unknown (others) / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 4.18 Å3/Da / Density % sol: 75.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 2050, 200 mM (NH4)2SO4, and 100 mM Na-cacodylate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→45.3035787427 Å / Num. obs: 30575 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 56.2225799317 Å2 / Rrim(I) all: 0.265 / Net I/σ(I): 11.1
Reflection shellResolution: 3.05→3.16 Å / Num. unique obs: 3009 / CC1/2: 0.603

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.10010233314→45.3035787427 Å / SU ML: 0.363370378341 / Cross valid method: FREE R-VALUE / σ(F): 1.35849684192 / Phase error: 34.0190314619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.29944639389 1218 5.18033344675 %
Rwork0.25595945925 22294 -
obs0.2582532316 23512 78.8596344122 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.7091954344 Å2
Refinement stepCycle: LAST / Resolution: 3.10010233314→45.3035787427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 1 0 5741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002054836171785886
X-RAY DIFFRACTIONf_angle_d0.5317813198087983
X-RAY DIFFRACTIONf_chiral_restr0.0389492552152868
X-RAY DIFFRACTIONf_plane_restr0.00394209777981018
X-RAY DIFFRACTIONf_dihedral_angle_d8.896725640443928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.22420.251242745542470.262970465543720X-RAY DIFFRACTION23.6363636364
3.2242-3.37090.308693766566790.2946412226691366X-RAY DIFFRACTION44.162591687
3.3709-3.54850.318001681132930.2882352342051967X-RAY DIFFRACTION63.1514408338
3.5485-3.77080.3262176289091270.27501573032498X-RAY DIFFRACTION80.2261613692
3.7708-4.06170.3318211868251630.2561377741753021X-RAY DIFFRACTION96.8369829684
4.0617-4.47020.2917690089291650.2186445476043139X-RAY DIFFRACTION100
4.4702-5.11620.2300917394511830.2102946273413133X-RAY DIFFRACTION100
5.1162-6.4430.3132564680161740.2633346855573177X-RAY DIFFRACTION100
6.443-45.30840.3181110500121870.2850305954763273X-RAY DIFFRACTION98.9702517162
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.599209497150.480951113250.03840082930243.463925646230.253637055482.047428637270.114722766186-0.0201103999919-0.0284791622546-0.522648269601-0.1003793668430.3344688116580.133220359356-0.182191069968-0.02165562100930.1690630000920.0599837192298-0.02491141109940.187920408722-0.038836412173-0.0204002927313-54.5305420545-1.1777802846813.3846748458
20.383002357785-0.4299569528330.5729177694430.512643242504-0.6254385331940.8426055384620.2108721441220.329661695840.795973451674-0.277262541105-0.0597410582632-0.390575366946-0.472839871145-0.590187723461-0.1086018608710.4840148111860.2796487649660.4211808452810.6308546580820.3333507267860.802115901545-40.9973819077-76.326375676814.7772480328
32.51835144507-1.209782302931.242668636321.62597136420.4171156253921.55134432833-0.2359807750660.6632902549890.406104718977-0.177202275555-0.701228464766-0.77477595645-0.305327950882-0.02005692720290.03982886682120.2154135414590.08437980418290.3485107464570.5606894791450.01011081243840.534238127326-33.2643041523-55.779175076818.3542644772
42.219175823080.572841410055-0.7448548804933.16029414458-0.3544003671591.312996355340.02411022928120.3881347276650.214184704761-0.480174938940.0583370436916-0.0663527418703-0.04716099983720.0892907474579-0.0883686680796-0.0645037956885-0.01380460766420.2515589967990.395582144260.0544702003264-0.0139013621649-30.99130183181.8824202594522.3265074896
50.03201521050610.447523194394-0.2475429521722.63019711678-1.004417995810.143553059256-0.1688682918160.2133742621230.03071312693890.5600755701550.131492389139-0.049001321478-0.293601486870.0568341005262-0.2066160239990.2145116656850.1492980910710.2225155090460.341247213561-0.1818508734390.710424467366-28.8397968755-53.262274349233.8067233582
62.063841345480.0882212880432-0.3435940941264.176122293361.037273587771.304295133550.103338269048-0.2179812474780.4244366863120.0773633349037-0.04000002571030.474249964203-0.153858686792-0.143995082759-0.03259800019870.0967363149089-0.03632834147350.06521072014420.282567411297-0.03145903831740.491660710019-22.0539523235-112.92835000421.670444925
73.870250507413.966866523321.209592025967.876847474621.830926150711.70780215643-0.3686077526730.770909109888-1.18211451404-0.8697965449720.1291091518410.1541765372731.39478266423-0.9424665798670.2678291758311.34469237904-0.221436971471-0.0641546175480.949085045012-0.3682128649041.16308869586-53.9218069693-112.3493852188.39499013903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 100 through 288 )
2X-RAY DIFFRACTION2chain 'A' and (resid 289 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 398 )
4X-RAY DIFFRACTION4chain 'B' and (resid 101 through 255 )
5X-RAY DIFFRACTION5chain 'B' and (resid 256 through 400 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 118 )
7X-RAY DIFFRACTION7chain 'E' and (resid 2 through 118 )

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