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Yorodumi- PDB-4xtb: Crystal structure of the N-terminal domain of the human mitochond... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xtb | ||||||
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Title | Crystal structure of the N-terminal domain of the human mitochondrial calcium uniporter | ||||||
Components | Calcium uniporter protein, mitochondrial | ||||||
Keywords | TRANSPORT PROTEIN / Calcium channel / Membrane protein / Mitochondria | ||||||
Function / homology | Function and homology information uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission ...uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / 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: 1.5 Å | ||||||
Authors | Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.-S. ...Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.-S. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / Park, Z.Y. / Kim, Y.-S. / Wang, J. / Kim, D.H. / Eom, S.H. | ||||||
Citation | Journal: Embo Rep. / Year: 2015 Title: Structure and function of the N-terminal domain of the human mitochondrial calcium uniporter. Authors: Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.S. / Lee, J.G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / ...Authors: Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.S. / Lee, J.G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / Park, Z.Y. / Kim, Y.S. / Wang, J. / Kim, D.H. / 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 | 4xtb.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xtb.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xtb_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 4xtb_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 4xtb_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4xtb_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/4xtb ftp://data.pdbj.org/pub/pdb/validation_reports/xt/4xtb | HTTPS FTP |
-Related structure data
Related structure data | 4xsjSC 5bz6C S: Starting model for refinement C: citing same article (ref.) |
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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: 14085.148 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 75-185) 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-PG4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.55 M lithium sulphate 0.1 M Bis-Tris propane (pH 8.0) PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→100 Å / Num. obs: 23888 / % possible obs: 99.4 % / Redundancy: 5 % / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.37→1.39 Å / Mean I/σ(I) obs: 1.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XSJ Resolution: 1.5→48.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.308 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.218 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→48.03 Å
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Refine LS restraints |
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