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- PDB-9e2p: Complex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613) -

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Basic information

Entry
Database: PDB / ID: 9e2p
TitleComplex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613)
Components
  • Mitochondrial Rho GTPase 1
  • Trafficking kinesin protein 1
KeywordsCYTOSOLIC PROTEIN / mitochondrial transport
Function / homology
Function and homology information


anterograde axonal transport of mitochondrion / RHOT1 GTPase cycle / mitochondrion distribution / mitochondrial outer membrane permeabilization / GABA receptor binding / cellular homeostasis / vesicle transport along microtubule / regulation of mitochondrion organization / mitochondrion transport along microtubule / endosome to lysosome transport ...anterograde axonal transport of mitochondrion / RHOT1 GTPase cycle / mitochondrion distribution / mitochondrial outer membrane permeabilization / GABA receptor binding / cellular homeostasis / vesicle transport along microtubule / regulation of mitochondrion organization / mitochondrion transport along microtubule / endosome to lysosome transport / myosin binding / protein targeting / neurogenesis / axon cytoplasm / mitochondrion organization / cytoplasmic vesicle / 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 / dendrite / GTP binding / mitochondrion / membrane
Similarity search - Function
HAP1, N-terminal / Trafficking kinesin-binding protein, C-terminal / : / HAP1 N-terminal conserved region / Kinesin associated protein / Kinesin associated protein / HAP1 N-terminal conserved region / Mitochondrial Rho GTPase 1/3, EF hand associated, type-1 / EF hand associated, type-2 / MIRO domain ...HAP1, N-terminal / Trafficking kinesin-binding protein, C-terminal / : / HAP1 N-terminal conserved region / Kinesin associated protein / Kinesin associated protein / HAP1 N-terminal conserved region / 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. / 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, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Trafficking kinesin protein 1 / Mitochondrial Rho GTPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsRavitch, E.E. / Baltrusaitis, E.E. / Barrie, K.R. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1 GM136511 United States
CitationJournal: To Be Published
Title: Complex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613)
Authors: Ravitch, E.E. / Baltrusaitis, E.E. / Perez, T.P. / Barrie, K.R. / Fenton, A.R. / Holbaur, E.L.F. / Dominguez, R.
History
DepositionOct 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial Rho GTPase 1
B: Trafficking kinesin protein 1
C: Mitochondrial Rho GTPase 1
D: Trafficking kinesin protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,59414
Polymers155,2934
Non-polymers2,30210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Mitochondrial Rho GTPase 1 / MIRO-1 / hMiro-1 / Rac-GTP-binding protein-like protein / Ras homolog gene family member T1


Mass: 71050.766 Da / Num. of mol.: 2
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
#2: Protein Trafficking kinesin protein 1


Mass: 6595.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C9AJS8
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)
Type: COMPLEX
Details: Complex was cross linked with glutaraldehyde and isolated by glycerol gradient cosedimentation
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 326239 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01710516
ELECTRON MICROSCOPYf_angle_d1.59514312
ELECTRON MICROSCOPYf_dihedral_angle_d16.9061420
ELECTRON MICROSCOPYf_chiral_restr0.0621612
ELECTRON MICROSCOPYf_plane_restr0.0091818

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