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- PDB-6lb8: Crystal structure of the Ca2+-free T4L-MICU1-MICU2 complex -

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Basic information

Entry
Database: PDB / ID: 6lb8
TitleCrystal structure of the Ca2+-free T4L-MICU1-MICU2 complex
Components
  • Calcium uptake protein 2, mitochondrial
  • Endolysin,Calcium uptake protein 1, mitochondrial
KeywordsMETAL BINDING PROTEIN / Calcium binding protein / Mitochondrial / Uniporter / EF-hand
Function / homology
Function and homology information


negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / 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 / calcium ion import ...negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / 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 / calcium ion import / viral release from host cell by cytolysis / calcium channel complex / peptidoglycan catabolic process / mitochondrial membrane / protein homooligomerization / defense response / 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 / identical protein binding
Similarity search - Function
Calcium uptake protein 1/2/3 / EF hand / 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 1, calcium-binding site ...Calcium uptake protein 1/2/3 / EF hand / 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 1, calcium-binding site / EF-hand calcium-binding domain. / 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 / Calcium uptake protein 1, mitochondrial
Similarity search - Component
Biological speciesEscherichia virus T4
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.283 Å
AuthorsWu, W. / Shen, Q. / Zheng, J. / Jia, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21773014 China
Citation
Journal: Embo J. / Year: 2020
Title: The structure of the MICU1-MICU2 complex unveils the regulation of the mitochondrial calcium uniporter.
Authors: Wu, W. / Shen, Q. / Zhang, R. / Qiu, Z. / Wang, Y. / Zheng, J. / Jia, Z.
#1: Journal: Embo Rep. / Year: 2019
Title: The crystal structure of MICU2 provides insight into Ca 2+ binding and MICU1-MICU2 heterodimer formation.
Authors: Wu, W. / Shen, Q. / Lei, Z. / Qiu, Z. / Li, D. / Pei, H. / Zheng, J. / Jia, Z.
History
DepositionNov 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Endolysin,Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial
C: Endolysin,Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)198,0824
Polymers198,0824
Non-polymers00
Water0
1
A: Endolysin,Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)99,0412
Polymers99,0412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-19 kcal/mol
Surface area38550 Å2
MethodPISA
2
C: Endolysin,Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)99,0412
Polymers99,0412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-17 kcal/mol
Surface area38550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.339, 133.296, 178.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endolysin,Calcium uptake protein 1, mitochondrial / Lysis protein / Lysozyme / Muramidase / Atopy-related autoantigen CALC / ara CALC / Calcium-binding ...Lysis protein / Lysozyme / Muramidase / Atopy-related autoantigen CALC / ara CALC / Calcium-binding atopy-related autoantigen 1


Mass: 60321.707 Da / Num. of mol.: 2 / Mutation: C54T,C97A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of T4L Endolysin, Linker, and Calcium uptake protein 1
Source: (gene. exp.) Escherichia virus T4, (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, MICU1, CALC, CBARA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9IEF7, UniProt: Q9BPX6, lysozyme
#2: Protein Calcium uptake protein 2, mitochondrial / EF-hand domain-containing family member A1


Mass: 38719.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IYU8

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2% tacsimate pH 5.0, 0.1 M sodium citrate pH 5.0, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.283→49.06 Å / Num. obs: 29560 / % possible obs: 99 % / Redundancy: 13 % / CC1/2: 0.958 / Rmerge(I) obs: 0.1947 / Rrim(I) all: 0.2028 / Net I/σ(I): 15.12
Reflection shellResolution: 3.283→3.401 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.505 / Num. unique obs: 2680 / CC1/2: 0.937 / Rrim(I) all: 0.5255 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000v705cdata reduction
HKL-3000v705cdata scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSC, 6IIH

4nsc

6iih


Resolution: 3.283→49.056 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1992 6.81 %
Rwork0.1835 27251 -
obs0.188 29243 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.61 Å2 / Biso mean: 39.8777 Å2 / Biso min: 4.94 Å2
Refinement stepCycle: final / Resolution: 3.283→49.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12694 0 0 0 12694
Num. residues----1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412928
X-RAY DIFFRACTIONf_angle_d1.29417313
X-RAY DIFFRACTIONf_chiral_restr0.071862
X-RAY DIFFRACTIONf_plane_restr0.012224
X-RAY DIFFRACTIONf_dihedral_angle_d21.0177790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2833-3.36540.35741270.2249173990
3.3654-3.45630.29831420.20141937100
3.4563-3.5580.28311410.20571920100
3.558-3.67280.26871410.19561923100
3.6728-3.8040.27961430.18491957100
3.804-3.95630.26331430.1751953100
3.9563-4.13630.2421420.17611937100
4.1363-4.35420.22651430.17211944100
4.3542-4.62680.21011430.15711971100
4.6268-4.98370.20571450.16231968100
4.9837-5.48470.25151430.18131951100
5.4847-6.27690.2641470.20552007100
6.2769-7.90290.25991470.20822016100
7.9029-49.0560.21981450.1712202896

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