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- PDB-6le5: Crystal structure of the mitochondrial calcium uptake 1 and 2 het... -

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Basic information

Entry
Database: PDB / ID: 6le5
TitleCrystal structure of the mitochondrial calcium uptake 1 and 2 heterodimer (MICU1-MICU2 heterodimer) in an apo state
Components
  • Calcium uptake protein 1, mitochondrial
  • Calcium uptake protein 2, mitochondrial
KeywordsMETAL BINDING PROTEIN / Complex / Mitochondrial calcium uptake 1 and mitochondrial calcium uptake 2
Function / homology
Function and homology information


mitochondrial crista junction / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / positive regulation of cristae formation / mitochondrial calcium ion transmembrane transport / uniplex complex / Processing of SMDT1 / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis ...mitochondrial crista junction / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / positive regulation of cristae formation / mitochondrial calcium ion transmembrane transport / uniplex complex / Processing of SMDT1 / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium ion sensor activity / cellular response to calcium ion starvation / calcium ion import / calcium channel inhibitor activity / calcium channel complex / Mitochondrial protein degradation / cellular response to calcium ion / calcium channel regulator activity / defense response / protein homooligomerization / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein 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
Calcium uptake protein 2, mitochondrial / Calcium uptake protein 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsPark, J. / Lee, Y. / Park, T. / Kang, J.Y. / Jin, M. / Yang, J. / Eom, S.H.
CitationJournal: Iucrj / Year: 2020
Title: Structure of the MICU1-MICU2 heterodimer provides insights into the gatekeeping threshold shift.
Authors: Park, J. / Lee, Y. / Park, T. / Kang, J.Y. / Mun, S.A. / Jin, M. / Yang, J. / Eom, S.H.
History
DepositionNov 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial
C: Calcium uptake protein 2, mitochondrial
D: Calcium uptake protein 1, mitochondrial
E: Calcium uptake protein 1, mitochondrial
F: Calcium uptake protein 2, mitochondrial
G: Calcium uptake protein 1, mitochondrial
H: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)318,0788
Polymers318,0788
Non-polymers00
Water00
1
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)79,5202
Polymers79,5202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-19 kcal/mol
Surface area27090 Å2
MethodPISA
2
C: Calcium uptake protein 2, mitochondrial
D: Calcium uptake protein 1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)79,5202
Polymers79,5202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-20 kcal/mol
Surface area29270 Å2
MethodPISA
3
E: Calcium uptake protein 1, mitochondrial
F: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)79,5202
Polymers79,5202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-20 kcal/mol
Surface area29080 Å2
MethodPISA
4
G: Calcium uptake protein 1, mitochondrial
H: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)79,5202
Polymers79,5202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-19 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.970, 173.720, 148.000
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Calcium uptake protein 1, mitochondrial / Atopy-related autoantigen CALC / ara CALC / Calcium-binding atopy-related autoantigen 1


Mass: 40204.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPX6
#2: Protein
Calcium uptake protein 2, mitochondrial / EF-hand domain-containing family member A1


Mass: 39314.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYU8
Has ligand of interestN
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG3350 0.2 M Ammonium citrate tribasic (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→86.86 Å / Num. obs: 57570 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.992 / Net I/σ(I): 6.2
Reflection shellResolution: 3.1→3.18 Å / Num. unique obs: 4480 / CC1/2: 0.258

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Cootmodel building
SHELXphasing
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.85 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33162 2802 4.9 %RANDOM
Rwork0.29277 ---
obs0.29467 54709 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å20.43 Å2
2---2.05 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17392 0 0 0 17392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01917731
X-RAY DIFFRACTIONr_bond_other_d00.0216234
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9523848
X-RAY DIFFRACTIONr_angle_other_deg3.663337044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59852175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37323.617857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.649152813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.47615106
X-RAY DIFFRACTIONr_chiral_restr0.0740.22636
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220143
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5987.6278826
X-RAY DIFFRACTIONr_mcbond_other4.5987.6278825
X-RAY DIFFRACTIONr_mcangle_it6.87211.41210959
X-RAY DIFFRACTIONr_mcangle_other6.87211.41210960
X-RAY DIFFRACTIONr_scbond_it8.0657.4388905
X-RAY DIFFRACTIONr_scbond_other8.0647.4388906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.08111.11312890
X-RAY DIFFRACTIONr_long_range_B_refined9.51659.26520474
X-RAY DIFFRACTIONr_long_range_B_other9.51659.26620475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 218 -
Rwork0.409 4018 -
obs--99.95 %

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