+Open data
-Basic information
Entry | Database: PDB / ID: 5ku1 | ||||||
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Title | hMiro1 EF hand and cGTPase domains in the GDP-bound state | ||||||
Components | Mitochondrial Rho GTPase 1 | ||||||
Keywords | HYDROLASE / Miro / GTPase / Parkin / Mitochondria | ||||||
Function / homology | Function and homology information RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / small GTPase-mediated signal transduction / mitochondrion organization / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane ...RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / small GTPase-mediated signal transduction / mitochondrion organization / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / Ub-specific processing proteases / GTPase activity / calcium ion binding / GTP binding / signal transduction / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Klosowiak, J.L. / Focia, P.J. / Rice, S.E. / Freymann, D.M. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural insights into Parkin substrate lysine targeting from minimal Miro substrates. Authors: Klosowiak, J.L. / Park, S. / Smith, K.P. / French, M.E. / Focia, P.J. / Freymann, D.M. / Rice, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ku1.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ku1.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ku1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ku1_validation.pdf.gz | 784.5 KB | Display | wwPDB validaton report |
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Full document | 5ku1_full_validation.pdf.gz | 789.1 KB | Display | |
Data in XML | 5ku1_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5ku1_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5ku1 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5ku1 | HTTPS FTP |
-Related structure data
Related structure data | 5ksoC 5kspC 5ksyC 5kszC 5ktyC 5kutC 4c0lS 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: 49065.859 Da / Num. of mol.: 1 / Fragment: hand and cGTPase domains (UNP residues 177-592) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOT1, ARHT1 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IXI2, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement | ||||
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#2: Chemical | ChemComp-GDP / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 9 mg/mL protein, 5 mM magnesium chloride, 1 mM GDP, 0.2 M ammonium sulfate, 0.1 M trisodium citrate, pH 5.6, 25% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 21325 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 30.5 |
Reflection shell | Highest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4C0L Resolution: 2.501→29.806 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→29.806 Å
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Refine LS restraints |
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LS refinement shell |
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