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- PDB-4c0j: Crystal structure of Drosophila Miro EF hand and cGTPase domains ... -

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Basic information

Entry
Database: PDB / ID: 4c0j
TitleCrystal structure of Drosophila Miro EF hand and cGTPase domains in the apo state (Apo-MiroS)
ComponentsMITOCHONDRIAL RHO GTPASE
KeywordsHYDROLASE / MITOCHONDRIAL TRANSPORT / CALCIUM-BINDING GTPASE / KINESIN / MITOPHAGY / HIDDEN EF HANDS
Function / homology
Function and homology information


RHOT2 GTPase cycle / RHOT1 GTPase cycle / anterograde axonal transport of mitochondrion / Ub-specific processing proteases / mitochondrial outer membrane permeabilization / regulation of mitochondrion organization / mitochondrion transport along microtubule / axonal transport of mitochondrion / axon cytoplasm / mitochondrion organization ...RHOT2 GTPase cycle / RHOT1 GTPase cycle / anterograde axonal transport of mitochondrion / Ub-specific processing proteases / mitochondrial outer membrane permeabilization / regulation of mitochondrion organization / mitochondrion transport along microtubule / axonal transport of mitochondrion / axon cytoplasm / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / GTPase activity / calcium ion binding / GTP binding / magnesium ion binding
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. / 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. / 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
L-HOMOSERINE / Mitochondrial Rho GTPase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)49,6458
Polymers49,1191
Non-polymers5267
Water1,06359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.930, 81.930, 155.821
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 201-617
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 / 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.: 4 / 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-HSE / L-HOMOSERINE


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


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsL-HOMOSERINE (HSE): UNIDENTIFIED LIGAND MODELED AS HOMOSERINE. UNIDENTIFIED ATOM (UNX): UNIDENTIFIED FEATURE

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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: 3.2 Å3/Da / Density % sol: 61 %
Description: MOLECULAR REPLACEMENT MODEL WAS A MIRO STRUCTURE DETERMINED BY SAD PHASING OF SEMET-LABELED PROTEIN.
Crystal growpH: 7.6
Details: 5.0MG/ML MIROS, 1.7M LISO4, 0.1M BIS-TRIS PH 7.6, 5MM EGTA

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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: Nov 14, 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: 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 shellResolution: 2.82→2.89 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.5 / % 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: 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.
RfactorNum. reflection% reflection
Rfree0.2617 2808 10 %
Rwork0.2247 --
obs0.2285 15051 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.49 Å2
Refinement stepCycle: LAST / Resolution: 2.82→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 30 59 3312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033333
X-RAY DIFFRACTIONf_angle_d0.5244513
X-RAY DIFFRACTIONf_dihedral_angle_d11.2911239
X-RAY DIFFRACTIONf_chiral_restr0.04493
X-RAY DIFFRACTIONf_plane_restr0.002577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8201-2.86870.37581370.31051234X-RAY DIFFRACTION98
2.8687-2.92080.33491300.30471302X-RAY DIFFRACTION99
2.9208-2.9770.39921480.31671234X-RAY DIFFRACTION100
2.977-3.03770.44831420.30161316X-RAY DIFFRACTION99
3.0377-3.10370.38831380.27861222X-RAY DIFFRACTION99
3.1037-3.17590.33521460.27671253X-RAY DIFFRACTION99
3.1759-3.25520.35231390.2681260X-RAY DIFFRACTION99
3.2552-3.34320.40631410.25571231X-RAY DIFFRACTION99
3.3432-3.44150.25441520.24631267X-RAY DIFFRACTION99
3.4415-3.55240.29391380.23841282X-RAY DIFFRACTION99
3.5524-3.67930.37751360.31551199X-RAY DIFFRACTION96
3.6793-3.82640.31341390.2511201X-RAY DIFFRACTION95
3.8264-4.00030.261320.21541241X-RAY DIFFRACTION98
4.0003-4.21090.22191490.19211268X-RAY DIFFRACTION100
4.2109-4.47420.2421360.17891274X-RAY DIFFRACTION100
4.4742-4.81880.18721540.18821269X-RAY DIFFRACTION100
4.8188-5.30220.17831300.18781272X-RAY DIFFRACTION100
5.3022-6.06580.23791440.21511265X-RAY DIFFRACTION100
6.0658-7.62880.21591390.21411263X-RAY DIFFRACTION100
7.6288-34.5940.20191380.18361269X-RAY DIFFRACTION99

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