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- PDB-8urg: Human mitochondrial calcium uniporter crystal structure (residues... -

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Basic information

Entry
Database: PDB / ID: 8urg
TitleHuman mitochondrial calcium uniporter crystal structure (residues 74-165 resolved) with lithium
ComponentsCalcium uniporter protein, mitochondrial
KeywordsMETAL TRANSPORT / Beta-grasp fold
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: 1.63 Å
AuthorsGrainger, R. / Colussi, D.C. / Noble, M. / Junop, M. / Stathopulos, P.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)438225 Canada
CitationJournal: Comput Struct Biotechnol J / Year: 2025
Title: Disrupting the network of co-evolving amino terminal domain residues relieves mitochondrial calcium uptake inhibition by MCUb.
Authors: Colussi, D.M. / Grainger, R. / Noble, M. / Lake, T. / Junop, M. / Stathopulos, P.B.
History
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.520, 55.520, 69.110
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3-CodonPlus / References: UniProt: Q8NE86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Imidazole (pH 8.0), 150 mM Li2So4, 30% w/v PEG3000, 4% v/v Formamide 1:2 drop ratio of protein to condition over 500 uL of 1.5 M ammonium sulfate Equimolar ratio of MCU 72-189 and MCUb ...Details: 50 mM Imidazole (pH 8.0), 150 mM Li2So4, 30% w/v PEG3000, 4% v/v Formamide 1:2 drop ratio of protein to condition over 500 uL of 1.5 M ammonium sulfate Equimolar ratio of MCU 72-189 and MCUb 59-159 for protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5212 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5212 Å / Relative weight: 1
ReflectionResolution: 1.63→48.08 Å / Num. obs: 15144 / % possible obs: 99.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Net I/σ(I): 13.3
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.885 / Mean I/σ(I) obs: 1 / Num. unique obs: 770 / CC1/2: 0.47 / Rpim(I) all: 1.059 / Rrim(I) all: 2.175 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→48.08 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 727 5.09 %
Rwork0.1988 --
obs0.2003 14271 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 0 0 126 844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01743
X-RAY DIFFRACTIONf_angle_d1.3291016
X-RAY DIFFRACTIONf_dihedral_angle_d14.549281
X-RAY DIFFRACTIONf_chiral_restr0.085122
X-RAY DIFFRACTIONf_plane_restr0.013133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.720.46161130.44651938X-RAY DIFFRACTION64
1.72-1.90.32881380.27572559X-RAY DIFFRACTION85
1.9-2.170.221550.19892948X-RAY DIFFRACTION97
2.17-2.740.22311600.18033020X-RAY DIFFRACTION100
2.74-48.080.18611610.16863079X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.0179 Å / Origin y: 6.0189 Å / Origin z: -4.6985 Å
111213212223313233
T0.0415 Å2-0.0027 Å2-0.0006 Å2-0.0421 Å20.0071 Å2--0.04 Å2
L0.6111 °2-0.1171 °20.1792 °2-0.6309 °2-0.3535 °2--0.3414 °2
S-0.0132 Å °0.0317 Å °-0.0112 Å °0.0552 Å °-0.0159 Å °-0.0315 Å °0.002 Å °-0.0011 Å °0 Å °
Refinement TLS groupSelection details: all

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