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- PDB-4c0k: Crystal structure of Drosophila Miro EF hand and cGTPase domains ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c0k | |||||||||
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Title | Crystal structure of Drosophila Miro EF hand and cGTPase domains bound to one calcium ion (Ca-MiroS) | |||||||||
![]() | MITOCHONDRIAL RHO GTPASE | |||||||||
![]() | HYDROLASE / MITOCHONDRIAL TRANSPORT / CALCIUM-BINDING GTPASE / KINESIN / MITOPHAGY / HIDDEN EF HANDS | |||||||||
Function / homology | ![]() establishment of mitochondrion localization, microtubule-mediated / RHOT2 GTPase cycle / RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / Ub-specific processing proteases / mitochondrion localization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / synaptic vesicle transport ...establishment of mitochondrion localization, microtubule-mediated / RHOT2 GTPase cycle / RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / Ub-specific processing proteases / mitochondrion localization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / synaptic vesicle transport / small GTPase-mediated signal transduction / axonal transport of mitochondrion / axon cytoplasm / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule cytoskeleton organization / mitochondrial outer membrane / GTPase activity / calcium ion binding / GTP binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Klosowiak, J.L. / Focia, P.J. / Wawrzak, Z. / Chakravarthy, S. / Landahl, E.C. / Freymann, D.M. / Rice, S.E. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.7 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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 Source: (gene. exp.) ![]() ![]() Description: DROSOPHILA GENOMICS RESOURCE CENTER CLONE RE22983 Production host: ![]() ![]() References: UniProt: Q8IMX7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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-Non-polymers , 6 types, 77 molecules ![](data/chem/img/HSE.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HSE / | ||||||
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#3: Chemical | ChemComp-UNX / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | UNKNOWN ATOM OR ION (UNX): UNIDENTIFI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % Description: MOLECULAR REPLACEMENT MODEL WAS A MIRO STRUCTURE DETERMINED BY SAD PHASING OF SE-MET LABELED PROTEIN. |
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Crystal grow | pH: 7.4 Details: 5.0MG/ML MIROS, 1.7 M LISO4, 0.1 M BIS-TRIS PH 7.4, 5 MM EGTA; CRYSTAL SOAKED IN 10MM CACL2 FOR 72H PRIOR TO DATA COLLECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 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: 2.8→42.1 Å / Num. obs: 15693 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 67.65 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: INITIAL MODEL FROM PRIOR DATASET Resolution: 2.801→42.075 Å / SU ML: 0.39 / σ(F): 1.91 / Phase error: 26.98 / 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: 47.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→42.075 Å
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Refine LS restraints |
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LS refinement shell |
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