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Yorodumi- PDB-5kuj: Human mitochondrial calcium uniporter (residues 72-189) crystal s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kuj | ||||||
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Title | Human mitochondrial calcium uniporter (residues 72-189) crystal structure with magnesium. | ||||||
Components | Calcium uniporter protein, mitochondrial | ||||||
Keywords | METAL TRANSPORT / beta-grasp fold N-terminal domain residues 72-189 mitochondrial calcium uniporter | ||||||
Function / homology | Function and homology information uniporter activity / 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 / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission ...uniporter activity / 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 / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / calcium channel complex / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / glucose homeostasis / protein complex oligomerization / mitochondrial inner membrane / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mok, M.C.Y. / Lee, S.K. / Junop, M.S. / Stathopulos, P.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Cell Chem Biol / Year: 2016 Title: Structural Insights into Mitochondrial Calcium Uniporter Regulation by Divalent Cations. Authors: Lee, S.K. / Shanmughapriya, S. / Mok, M.C. / Dong, Z. / Tomar, D. / Carvalho, E. / Rajan, S. / Junop, M.S. / Madesh, M. / Stathopulos, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kuj.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kuj.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5kuj ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5kuj | HTTPS FTP |
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-Related structure data
Related structure data | 5kueSC 5kugC 5kuiC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13880.736 Da / Num. of mol.: 1 / Fragment: unp residues 72-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NE86 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.32 M magnesium chloride, 0.1 M Tris pH 8.5, 24 % PEG 400, 1.6 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→68.98 Å / Num. obs: 15893 / % possible obs: 99.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KUE Resolution: 1.6→47.943 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→47.943 Å
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Refine LS restraints |
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LS refinement shell |
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