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- PDB-9k6m: Crystal structure of the Dictyostelium discoideum mitochondrial c... -

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Basic information

Entry
Database: PDB / ID: 9k6m
TitleCrystal structure of the Dictyostelium discoideum mitochondrial calcium uptake protein (DdMICU)
ComponentsEF-hand domain-containing protein
KeywordsMETAL BINDING PROTEIN / MICU
Function / homology
Function and homology information


Mitochondrial calcium ion transport / uniplex complex / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / mitochondrial intermembrane space / calcium ion binding
Similarity search - Function
Calcium uptake protein 1/2/3 / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
EF-hand domain-containing protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsJin, M. / Yang, J. / Park, J. / Kim, H. / Eom, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C1006267 Korea, Republic Of
National Research Foundation (NRF, Korea)No. RS-2024-00344154 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2025
Title: Structure of MICU from non-metazoan Dictyostelium discoideum reveals unique characteristics.
Authors: Jin, M. / Yang, J. / Park, J. / Kim, H. / Eom, S.H.
History
DepositionOct 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EF-hand domain-containing protein
B: EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2048
Polymers84,9642
Non-polymers2406
Water1,40578
1
A: EF-hand domain-containing protein
B: EF-hand domain-containing protein
hetero molecules

A: EF-hand domain-containing protein
B: EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,40816
Polymers169,9274
Non-polymers48112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
Unit cell
Length a, b, c (Å)103.937, 103.937, 297.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein EF-hand domain-containing protein / mitochondrial calcium uptake protein


Mass: 42481.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0287825 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54JS1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MIB buffer (Molecular Dimensions) pH 5.5, 20% (w/v) PEG 1500, 10 mM 3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate (CHAPS), and 10 mM tris(2-carboxyethyl)phosphine (TCEP)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→49.6 Å / Num. obs: 28688 / % possible obs: 99.9 % / Redundancy: 25.4 % / CC1/2: 0.998 / Net I/σ(I): 18.5
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 3190 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHASERphasing
REFMAC5.8.0415refinement
PHENIX1.21refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→49.109 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.913 / SU B: 0.001 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.267
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.26 1408 5.008 %
Rwork0.2209 26709 -
all0.223 --
obs-28117 97.996 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.151 Å2-0 Å2-0 Å2
2--0.151 Å20 Å2
3----0.301 Å2
Refinement stepCycle: LAST / Resolution: 2.502→49.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 6 78 4271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.502-2.5670.3561070.28919680.29220750.8980.9351000.267
2.567-2.6370.3551100.29919250.30320350.8920.9331000.281
2.637-2.7130.332820.27918860.28119680.920.941000.258
2.713-2.7970.269980.26518120.26519100.9510.9491000.244
2.797-2.8880.252900.24417680.24418580.9550.9561000.222
2.888-2.9890.266720.21517340.21718060.9520.9671000.191
2.989-3.1010.256820.20916620.21117440.9540.971000.177
3.101-3.2270.376860.25215920.25816870.9260.96699.46650.2
3.227-3.370.324830.28214820.28516170.9460.9696.78420.219
3.37-3.5340.36750.24213750.24715460.920.96493.79040.19
3.534-3.7240.267650.24712320.24814620.9560.96388.71410.192
3.724-3.9490.261680.21912140.22114220.9530.97290.15470.175
3.949-4.2190.249840.17511770.1813160.970.98195.82070.155
4.219-4.5550.155480.15311750.15312380.9850.98798.78840.149
4.555-4.9850.203510.16210870.16411500.9820.98498.95650.157
4.985-5.5660.2490.189960.18110450.9740.9791000.175
5.566-6.4140.213610.2168720.2169340.9680.9799.89290.214
6.414-7.8220.222450.2127660.2138110.970.9691000.214
7.822-10.9240.195370.1616030.1636460.9820.98599.07120.182
10.924-49.1090.268150.283830.284140.9730.95196.13530.316

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