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Yorodumi- PDB-4xsj: Crystal structure of the N-terminal domain of the human mitochond... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xsj | ||||||
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Title | Crystal structure of the N-terminal domain of the human mitochondrial calcium uniporter fused with T4 lysozyme | ||||||
Components | Lysozyme,Calcium uniporter protein, mitochondrial | ||||||
Keywords | TRANSPORT PROTEIN / Membrane protein / Calcium channel / Mitochondria | ||||||
Function / homology | Function and homology information uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / 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 / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / viral release from host cell by cytolysis / calcium channel complex / peptidoglycan catabolic process / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / cell wall macromolecule catabolic process / lysozyme / protein complex oligomerization / glucose homeostasis / lysozyme activity / host cell cytoplasm / mitochondrial inner membrane / defense response to bacterium / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 4xsj.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xsj.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xsj_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
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Full document | 4xsj_full_validation.pdf.gz | 433.8 KB | Display | |
Data in XML | 4xsj_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 4xsj_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/4xsj ftp://data.pdbj.org/pub/pdb/validation_reports/xs/4xsj | HTTPS FTP |
-Related structure data
Related structure data | 4xtbC 5bz6C 2lzmS 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: 29788.135 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-161,UNP RESIDUES 75-165 / Mutation: D20N, C54T, C97A Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF LYSOZYME (1-161), LINKER GG, CALCIUM UNIPORTER PROTEIN (75-165), AND TAGS LEHHHHHH Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126, MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q8NE86, lysozyme | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 3350, 5% glycerol, 0.3 M ammonium sulphate and 0.1 M Bis-Tris-HCl (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 32604 / % possible obs: 97.9 % / Redundancy: 7.2 % / Net I/σ(I): 15.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LZM Resolution: 1.8→48.5 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.966 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.102 / 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: 29.253 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.5 Å
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Refine LS restraints |
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