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- PDB-6lb7: Crystal structure of the Ca2+-free and Ca2+-bound MICU1-MICU2 complex -

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Basic information

Entry
Database: PDB / ID: 6lb7
TitleCrystal structure of the Ca2+-free and Ca2+-bound MICU1-MICU2 complex
Components
  • Calcium uptake protein 1, mitochondrial
  • Calcium uptake protein 2, mitochondrial
KeywordsMETAL BINDING PROTEIN / Calcium binding protein / Mitochondrial / Uniporter / EF-hand
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 / MOLECULAR REPLACEMENT / Resolution: 2.101 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 / Derived calculations / Category: citation / citation_author / struct_conn
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 / _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
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

Downloads & links

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Assembly

Deposited unit
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial
C: Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,6876
Polymers163,6064
Non-polymers802
Water19,7801098
1
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8834
Polymers81,8032
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-20 kcal/mol
Surface area29160 Å2
MethodPISA
2
C: Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)81,8032
Polymers81,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-19 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.481, 107.721, 170.381
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 Calcium uptake protein 1, mitochondrial / Atopy-related autoantigen CALC / ara CALC / Calcium-binding atopy-related autoantigen 1


Mass: 43083.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1, CALC, CBARA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BPX6
#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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium chloride, 5% (w/v) polyethylene glycol (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 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.101→47.3 Å / Num. obs: 92168 / % possible obs: 98 % / Redundancy: 13 % / CC1/2: 0.984 / Rmerge(I) obs: 0.1246 / Rrim(I) all: 0.1297 / Net I/σ(I): 10.87
Reflection shellResolution: 2.101→2.176 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.192 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 8058 / CC1/2: 0.775 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000v716.1data scaling
PDB_EXTRACT3.25data extraction
HKL-2000v716.1data reduction
PHENIX1.10.1-2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSC, 6IIH

4nsc

6iih


Resolution: 2.101→47.3 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2267 2000 2.2 %
Rwork0.194 --
obs0.1947 90895 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.94 Å2 / Biso mean: 35.5483 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 2.101→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9893 0 2 1098 10993
Biso mean--28.51 37.79 -
Num. residues----1205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02110088
X-RAY DIFFRACTIONf_angle_d1.29213508
X-RAY DIFFRACTIONf_chiral_restr0.0631448
X-RAY DIFFRACTIONf_plane_restr0.0131736
X-RAY DIFFRACTIONf_dihedral_angle_d17.1376061
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.101-2.1530.23581230.2432548486
2.153-2.21130.30041380.2388608996
2.2113-2.27630.28961400.2362625698
2.2763-2.34980.25591430.2216635299
2.3498-2.43380.2411440.22016403100
2.4338-2.53120.23321420.22086351100
2.5312-2.64640.29061450.21896438100
2.6464-2.78590.24521440.21426395100
2.7859-2.96040.23911450.20746441100
2.9604-3.1890.23651450.19746435100
3.189-3.50980.19931460.18366471100
3.5098-4.01740.17661450.16426475100
4.0174-5.06060.19351480.15286570100
5.0606-47.30.23251520.189673599

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