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Yorodumi- PDB-4c0j: Crystal structure of Drosophila Miro EF hand and cGTPase domains ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c0j | |||||||||
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Title | Crystal structure of Drosophila Miro EF hand and cGTPase domains in the apo state (Apo-MiroS) | |||||||||
Components | MITOCHONDRIAL RHO GTPASE | |||||||||
Keywords | HYDROLASE / MITOCHONDRIAL TRANSPORT / CALCIUM-BINDING GTPASE / KINESIN / MITOPHAGY / HIDDEN EF HANDS | |||||||||
Function / homology | Function and homology information establishment of mitochondrion localization, microtubule-mediated / RHOT2 GTPase cycle / RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / Ub-specific processing proteases / mitochondrion localization / engulfment of apoptotic cell / cortical cytoskeleton organization / cellular homeostasis / motor neuron axon guidance ...establishment of mitochondrion localization, microtubule-mediated / RHOT2 GTPase cycle / RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / Ub-specific processing proteases / mitochondrion localization / engulfment of apoptotic cell / cortical cytoskeleton organization / cellular homeostasis / motor neuron axon guidance / regulation of mitochondrion organization / mitochondrion transport along microtubule / synaptic vesicle transport / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / axonal transport of mitochondrion / mitotic cytokinesis / axon cytoplasm / mitochondrion organization / actin filament organization / regulation of actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule cytoskeleton organization / regulation of cell shape / cytoplasmic vesicle / mitochondrial outer membrane / cytoskeleton / GTPase activity / calcium ion binding / GTP binding / protein kinase binding / magnesium ion binding / signal transduction Similarity search - Function | |||||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | |||||||||
Authors | Klosowiak, J.L. / Focia, P.J. / Wawrzak, Z. / Chakravarthy, S. / Landahl, E.C. / Freymann, D.M. / Rice, S.E. | |||||||||
Citation | Journal: Embo Rep. / Year: 2013 Title: Structural Coupling of the EF Hand and C-Terminal Gtpase Domains in the Mitochondrial Protein Miro. Authors: Klosowiak, J.L. / Focia, P.J. / Chakravarthy, S. / Landahl, E.C. / 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 | 4c0j.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c0j.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/4c0j ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c0j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49118.531 Da / Num. of mol.: 1 / Fragment: ELM1, ELM2, AND CGTPASE, RESIDUES 201-617 Source method: isolated from a genetically manipulated source Details: DROSOPHILA MIRO RESIDUES 201-617 / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) Description: DROSOPHILA GENOMICS RESOURCE CENTER CLONE RE22983 Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RP References: UniProt: Q8IMX7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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-Non-polymers , 5 types, 66 molecules
#2: Chemical | ChemComp-UNX / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-HSE / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | L-HOMOSERINE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % Description: MOLECULAR REPLACEMENT MODEL WAS A MIRO STRUCTURE DETERMINED BY SAD PHASING OF SEMET-LABELED PROTEIN. |
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Crystal grow | pH: 7.6 Details: 5.0MG/ML MIROS, 1.7M LISO4, 0.1M BIS-TRIS PH 7.6, 5MM EGTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 |
Radiation | Monochromator: C (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→41.9 Å / Num. obs: 15216 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.82→2.89 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INITIAL MODEL FROM PRIOR DATASET Resolution: 2.82→34.59 Å / SU ML: 0.39 / σ(F): 1.91 / Phase error: 32.38 / Stereochemistry target values: ML Details: REFINEMENT NUMBER OF REFLECTIONS TREATS ANOMALOUS PAIRS SEPARATELY. A LARGE LOOP COMPRISING RESIDUES 434-441 IS POORLY ORDERED, DESPITE THE SIDECHAINS OF I435 AND L437 CONTRIBUTING TO A ...Details: REFINEMENT NUMBER OF REFLECTIONS TREATS ANOMALOUS PAIRS SEPARATELY. A LARGE LOOP COMPRISING RESIDUES 434-441 IS POORLY ORDERED, DESPITE THE SIDECHAINS OF I435 AND L437 CONTRIBUTING TO A HYDROPHOBIC CRYSTAL CONTACT, AND A SECOND LOOP COMPRISING RESIDUES 561-566 IS ALSO POORLY ORDERED. RESIDUES OF BOTH HAVE BEEN BUILT AS ALA OR GLY WHERE SIDECHAIN POSITIONS COULD NOT BE DETERMINED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→34.59 Å
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Refine LS restraints |
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LS refinement shell |
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