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Yorodumi- PDB-6le5: Crystal structure of the mitochondrial calcium uptake 1 and 2 het... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6le5 | ||||||
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Title | Crystal structure of the mitochondrial calcium uptake 1 and 2 heterodimer (MICU1-MICU2 heterodimer) in an apo state | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Complex / Mitochondrial calcium uptake 1 and mitochondrial calcium uptake 2 | ||||||
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 / calcium channel complex / mitochondrial membrane / protein homooligomerization / defense response / mitochondrial intermembrane space / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | ||||||
Authors | Park, J. / Lee, Y. / Park, T. / Kang, J.Y. / Jin, M. / Yang, J. / Eom, S.H. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6le5.cif.gz | 444.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6le5.ent.gz | 368.5 KB | Display | PDB format |
PDBx/mmJSON format | 6le5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/6le5 ftp://data.pdbj.org/pub/pdb/validation_reports/le/6le5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG3350 0.2 M Ammonium citrate tribasic (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.1→3.18 Å / Num. unique obs: 4480 / CC1/2: 0.258 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.678 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→50.01 Å
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Refine LS restraints |
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