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- EMDB-47460: Complex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613) -

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Basic information

Entry
Database: EMDB / ID: EMD-47460
TitleComplex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613)
Map dataUnsharpened and sharpened maps averaged in Coot. Map used for model building and refinement.
Sample
  • Complex: Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)
    • Protein or peptide: Mitochondrial Rho GTPase 1
    • Protein or peptide: Trafficking kinesin protein 1
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
Keywordsmitochondrial transport / CYTOSOLIC PROTEIN
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
Trafficking kinesin protein 1 / Mitochondrial Rho GTPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsRavitch EE / Baltrusaitis EE / Barrie KR / Dominguez R
Funding support United States, 1 items
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 EE / Baltrusaitis EE / Perez TP / Barrie KR / Fenton AR / Holbaur ELF / Dominguez R
History
DepositionOct 22, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47460.png

Downloads & links

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Map

FileDownload / File: emd_47460.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened and sharpened maps averaged in Coot. Map used for model building and refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.24069731 - 0.36250794
Average (Standard dev.)0.000386872 (±0.00853756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47460_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_47460_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_47460_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_47460_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_47460_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)

EntireName: Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)
Components
  • Complex: Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)
    • Protein or peptide: Mitochondrial Rho GTPase 1
    • Protein or peptide: Trafficking kinesin protein 1
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)

SupramoleculeName: Heterotetrameric complex of MIRO1 and TRAK1 Binding Site-2 (L570-R613)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Complex was cross linked with glutaraldehyde and isolated by glycerol gradient cosedimentation
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitochondrial Rho GTPase 1

MacromoleculeName: Mitochondrial Rho GTPase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.050766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SENLYFQGSM KKDVRILLVG EPRVGKTSLI MSLVSEEFPE EVPPRAEEIT IPADVTPERV PTHIVDYSEA EQSDEQLHQ EISQANVICI VYAVNNKHSI DKVTSRWIPL INERTDKDSR LPLILVGNKS DLVEYSSMET ILPIMNQYTE I ETCVECSA ...String:
MGSSHHHHHH SENLYFQGSM KKDVRILLVG EPRVGKTSLI MSLVSEEFPE EVPPRAEEIT IPADVTPERV PTHIVDYSEA EQSDEQLHQ EISQANVICI VYAVNNKHSI DKVTSRWIPL INERTDKDSR LPLILVGNKS DLVEYSSMET ILPIMNQYTE I ETCVECSA KNLKNISELF YYAQKAVLHP TGPLYCPEEK EMKPACIKAL TRIFKISDQD NDGTLNDAEL NFFQRICFNT PL APQALED VKNVVRKHIS DGVADSGLTL KGFLFLHTLF IQRGRHETTW TVLRRFGYDD DLDLTPEYLF PLLKIPPDCT TEL NHHAYL FLQSTFDKHD LDRDCALSPD ELKDLFKVFP YIPWGPDVNN TVCTNERGWI TYQGFLSQWT LTTYLDVQRC LEYL GYLGY SILTEQESQA SAVTVTRDKK IDLQKKQTQR NVFRCNVIGV KNCGKSGVLQ ALLGRNLMRQ KKIREDHKSY YAINT VYVY GQEKYLLLHD ISESEFLTEA EIICDVVCLV YDVSNPKSFE YCARIFKQHF MDSRIPCLIV AAKSDLHEVK QEYSIS PTD FCRKHKMPPP QAFTCNTADA PSKDIFVKLT TMAMYPHVTQ ADLKSSTWSH PQFEK

UniProtKB: Mitochondrial Rho GTPase 1

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Macromolecule #2: Trafficking kinesin protein 1

MacromoleculeName: Trafficking kinesin protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.595561 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGHMYLPEKL QIVKPLEGSA TLHHWQQLAQ PHLGGILDPR PGVVTKGFRT LDVDLDEVY

UniProtKB: Trafficking kinesin protein 1

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio map generated in CryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326239
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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