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Yorodumi- PDB-5kug: Human mitochondrial calcium uniporter (residues 72-189) crystal s... -
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-Basic information
Entry | Database: PDB / ID: 5kug | ||||||
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Title | Human mitochondrial calcium uniporter (residues 72-189) crystal structure with lithium | ||||||
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 / uniplex complex / mitochondrial calcium ion transmembrane transport / 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 / uniplex complex / mitochondrial calcium ion transmembrane transport / 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 / protein complex oligomerization / glucose homeostasis / mitochondrial inner membrane / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 5kug.cif.gz | 35.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kug.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5kug ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5kug | HTTPS FTP |
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-Related structure data
Related structure data | 5kueSC 5kuiC 5kujC 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: 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: 2.25 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M lithium sulfate, 0.1 M imidazole pH 8.0, 10 % PEG 3000, 1.5 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: 1.5→48.13 Å / Num. obs: 19303 / % possible obs: 99.5 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KUE Resolution: 1.9→28.19 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.19 Å
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Refine LS restraints |
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LS refinement shell |
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