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- PDB-6iih: crystal structure of mitochondrial calcium uptake 2(MICU2) -

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Basic information

Entry
Database: PDB / ID: 6iih
Titlecrystal structure of mitochondrial calcium uptake 2(MICU2)
ComponentsEndolysin,Calcium uptake protein 2, mitochondrial
KeywordsCalcium Binding Protein / mitochondrial / EF-hand / T4L fusion protein / METAL BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of mitochondrial calcium ion concentration / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / viral release from host cell by cytolysis / calcium channel complex ...negative regulation of mitochondrial calcium ion concentration / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / viral release from host cell by cytolysis / calcium channel complex / peptidoglycan catabolic process / mitochondrial intermembrane space / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / mitochondrial inner membrane / host cell cytoplasm / defense response to bacterium / protein heterodimerization activity / calcium ion binding / mitochondrion
Similarity search - Function
Calcium uptake protein 1/2/3 / EF-hand domain pair / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain ...Calcium uptake protein 1/2/3 / EF-hand domain pair / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Calcium uptake protein 2, mitochondrial
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.958 Å
AuthorsShen, Q. / Wu, W. / Zheng, J. / Jia, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21773014 China
CitationJournal: Embo Rep. / Year: 2019
Title: The crystal structure of MICU2 provides insight into Ca2+binding and MICU1-MICU2 heterodimer formation.
Authors: Wu, W. / Shen, Q. / Lei, Z. / Qiu, Z. / Li, D. / Pei, H. / Zheng, J. / Jia, Z.
History
DepositionOct 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,5985
Polymers115,4782
Non-polymers1203
Water14,754819
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-36 kcal/mol
Surface area41990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.743, 96.311, 85.488
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57739.125 Da / Num. of mol.: 2 / Mutation: C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Plasmid: pET-28(b) / Gene: MICU2, EFHA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00720, UniProt: Q8IYU8, lysozyme
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.16
Details: 100 mM Sodium phosphate monobasic , 100 mM potassium phosphate monobasic , 100 mM MES, 6.0 and 1M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.958→48.676 Å / Num. obs: 73695 / % possible obs: 96 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.033 / Rrim(I) all: 0.058 / Χ2: 0.977 / Net I/av σ(I): 21.26 / Net I/σ(I): 8.98
Reflection shellResolution: 1.958→2.007 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 3701 / CC1/2: 0.692 / Rpim(I) all: 0.365 / Rrim(I) all: 0.629 / Χ2: 0.971 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000v716.1data reduction
HKL-2000v716.1data scaling
PHENIX(1.11.1_2575: 000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.958→48.676 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 2000 2.86 %
Rwork0.1796 --
obs0.1809 69963 91.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.958→48.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7256 0 3 819 8078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127399
X-RAY DIFFRACTIONf_angle_d1.1619917
X-RAY DIFFRACTIONf_dihedral_angle_d3.1274445
X-RAY DIFFRACTIONf_chiral_restr0.0571065
X-RAY DIFFRACTIONf_plane_restr0.0091266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9582-2.00710.285970.23773287X-RAY DIFFRACTION62
2.0071-2.06140.261200.22144111X-RAY DIFFRACTION78
2.0614-2.12210.26181400.21194730X-RAY DIFFRACTION89
2.1221-2.19060.27361440.20334886X-RAY DIFFRACTION92
2.1906-2.26880.23751490.19365092X-RAY DIFFRACTION96
2.2688-2.35970.2281520.1835147X-RAY DIFFRACTION97
2.3597-2.46710.24511530.17215195X-RAY DIFFRACTION97
2.4671-2.59710.23861510.17355128X-RAY DIFFRACTION97
2.5971-2.75980.21541490.17655088X-RAY DIFFRACTION95
2.7598-2.97290.2241490.17785072X-RAY DIFFRACTION96
2.9729-3.2720.25281520.1775137X-RAY DIFFRACTION96
3.272-3.74530.22821490.16695090X-RAY DIFFRACTION95
3.7453-4.71810.16991470.15074969X-RAY DIFFRACTION93
4.7181-48.69110.22411480.19085031X-RAY DIFFRACTION92

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