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- PDB-4c0l: Crystal structure of Drosophila Miro EF hand and cGTPase domains ... -

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Basic information

Entry
Database: PDB / ID: 4c0l
TitleCrystal structure of Drosophila Miro EF hand and cGTPase domains bound to one magnesium ion and Mg:GDP (MgGDP-MiroS)
ComponentsMITOCHONDRIAL RHO GTPASE
KeywordsHYDROLASE / 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 / regulation of actin cytoskeleton organization / actin filament 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
Mitochondrial Rho GTPase 1/3, EF hand associated, type-1 / EF hand associated, type-2 / MIRO domain / Mitochondrial Rho GTPase / EF hand associated / EF hand associated / Miro domain profile. / Small GTPase Rho / EF-hand / Recoverin; domain 1 ...Mitochondrial Rho GTPase 1/3, EF hand associated, type-1 / EF hand associated, type-2 / MIRO domain / Mitochondrial Rho GTPase / EF hand associated / EF hand associated / Miro domain profile. / Small GTPase Rho / EF-hand / Recoverin; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / L-HOMOSERINE / Mitochondrial Rho GTPase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKlosowiak, J.L. / Focia, P.J. / Wawrzak, Z. / Chakravarthy, S. / Landahl, E.C. / Freymann, D.M. / Rice, S.E.
CitationJournal: 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
DepositionAug 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOCHONDRIAL RHO GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,04110
Polymers49,1191
Non-polymers9229
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.510, 81.510, 154.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MITOCHONDRIAL RHO GTPASE / MIRO / DMIRO


Mass: 49118.531 Da / Num. of mol.: 1 / Fragment: ELM1, ELM2, AND CGTPASE, RESIDUES 201-467
Source method: isolated from a genetically manipulated source
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 , 7 types, 26 molecules

#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsUNKNOWN ATOM OR ION (UNX): UNIDENTIFIED FEATURE ASSIGNED AS UNX UNKNOWN ATOM OR ION. UNKNOWN LIGAND ...UNKNOWN ATOM OR ION (UNX): UNIDENTIFIED FEATURE ASSIGNED AS UNX UNKNOWN ATOM OR ION. UNKNOWN LIGAND (HSE): UNIDENTIFIED LIGAND MODELED AS HOMOSERINE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.48 %
Description: MOLECULAR REPLACEMENT MODEL WAS A MIRO STRUCTURE DETERMINED BY SAD PHASING OF SEMET-LABELED PROTEIN.
Crystal growpH: 8
Details: 5.0 MG/ML MIROS,1.9 M LISO4, 0.1 M BIS-TRIS PH 8.0, 5 MM EGTA; CRYSTALS WERE SOAKED IN 30 MM MGCL2, 20 MM GDP FOR 72H PRIOR TO DATA COLLECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→52.2 Å / Num. obs: 12487 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 82.19 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8
Reflection shellResolution: 3→3.24 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INITIAL MODEL FROM PRIOR DATASET

Resolution: 3→25.825 Å / SU ML: 0.41 / σ(F): 1.91 / Phase error: 33.27 / Stereochemistry target values: ML
Details: REFINEMENT NUMBER OF REFLECTIONS TREATS ANOMALOUS PAIRS SEPARATELY.
RfactorNum. reflection% reflection
Rfree0.2585 1107 4.9 %
Rwork0.2145 --
obs0.2166 12299 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.06 Å2
Refinement stepCycle: LAST / Resolution: 3→25.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 55 17 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033381
X-RAY DIFFRACTIONf_angle_d0.5234567
X-RAY DIFFRACTIONf_dihedral_angle_d9.8091261
X-RAY DIFFRACTIONf_chiral_restr0.04496
X-RAY DIFFRACTIONf_plane_restr0.002580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.13660.39681250.32692333X-RAY DIFFRACTION85
3.1366-3.30170.40711350.29512638X-RAY DIFFRACTION98
3.3017-3.50810.36741400.26312699X-RAY DIFFRACTION99
3.5081-3.77820.2471440.23282726X-RAY DIFFRACTION99
3.7782-4.1570.25861340.19882746X-RAY DIFFRACTION99
4.157-4.75520.25691420.18722738X-RAY DIFFRACTION100
4.7552-5.97880.20361420.21492717X-RAY DIFFRACTION100
5.9788-25.82590.23021450.19132716X-RAY DIFFRACTION99

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