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- PDB-6eaz: Apo structure of the mitochondrial calcium uniporter protein MICU2 -

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Basic information

Entry
Database: PDB / ID: 6eaz
TitleApo structure of the mitochondrial calcium uniporter protein MICU2
ComponentsCalcium uptake protein 2, mitochondrial
KeywordsMETAL BINDING PROTEIN / uniporter / calcium / EF hand / channel / mitochondria
Function / homology
Function and homology information


Mitochondrial calcium ion transport / Processing of SMDT1 / negative regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion transmembrane transport / uniplex complex / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity / calcium import into the mitochondrion / calcium channel complex ...Mitochondrial calcium ion transport / Processing of SMDT1 / negative regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion transmembrane transport / uniplex complex / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity / calcium import into the mitochondrion / calcium channel complex / mitochondrial intermembrane space / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion
Similarity search - Function
Calcium uptake protein 1/2/3 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calcium uptake protein 2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.504 Å
AuthorsKamer, K.J. / Grabarek, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Crystal structure of MICU2 and comparison with MICU1 reveal insights into the uniporter gating mechanism.
Authors: Kamer, K.J. / Jiang, W. / Kaushik, V.K. / Mootha, V.K. / Grabarek, Z.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Assembly

Deposited unit
A: Calcium uptake protein 2, mitochondrial
B: Calcium uptake protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,84510
Polymers89,1082
Non-polymers7378
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-23 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.562, 125.524, 72.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Calcium uptake protein 2, mitochondrial / EF-hand domain-containing family member A1


Mass: 44553.941 Da / Num. of mol.: 2 / Fragment: UNP residues 68-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Micu2, Efha1 / Plasmid: petduet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8CD10
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4% PEG3350, 150 mM tri-lithium citrate

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→83.81 Å / Num. obs: 35943 / % possible obs: 98.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 50.89 Å2 / Net I/σ(I): 14.8
Reflection shellResolution: 2.504→2.512 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.504→83.803 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1769 5.03 %
Rwork0.1984 --
obs0.201 35200 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.504→83.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 48 35 5601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075675
X-RAY DIFFRACTIONf_angle_d0.9037578
X-RAY DIFFRACTIONf_dihedral_angle_d16.583395
X-RAY DIFFRACTIONf_chiral_restr0.048796
X-RAY DIFFRACTIONf_plane_restr0.004955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.504-2.57170.33381190.31182421X-RAY DIFFRACTION93
2.5717-2.64740.35971390.2982489X-RAY DIFFRACTION98
2.6474-2.73290.34631270.28292604X-RAY DIFFRACTION99
2.7329-2.83050.28961210.25542556X-RAY DIFFRACTION99
2.8305-2.94390.33571330.24012555X-RAY DIFFRACTION98
2.9439-3.07790.31311450.22812541X-RAY DIFFRACTION98
3.0779-3.24010.33611330.22682589X-RAY DIFFRACTION99
3.2401-3.44310.29621440.21922589X-RAY DIFFRACTION99
3.4431-3.7090.25951280.19292569X-RAY DIFFRACTION98
3.709-4.08220.22861380.17942596X-RAY DIFFRACTION98
4.0822-4.67290.2391580.1622597X-RAY DIFFRACTION99
4.6729-5.88720.17671420.17212611X-RAY DIFFRACTION98
5.8872-83.84940.20341420.1732714X-RAY DIFFRACTION96

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