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- PDB-7vc9: Tom20 subunits -

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Basic information

Entry
Database: PDB / ID: 7vc9
TitleTom20 subunits
ComponentsMitochondrial import receptor subunit TOM20 homolog
KeywordsTRANSLOCASE / Tom20 / Cryo-EM
Function / homology
Function and homology information


tRNA import into mitochondrion / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane ...tRNA import into mitochondrion / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / sperm midpiece / PINK1-PRKN Mediated Mitophagy / cell periphery / unfolded protein binding / mitochondrial outer membrane / Ub-specific processing proteases / mitochondrion
Similarity search - Function
Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å
AuthorsLiu, D.S. / Sui, S.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: To Be Published
Title: Tom20 subunits
Authors: Liu, D.S. / Sui, S.F.
History
DepositionSep 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Mitochondrial import receptor subunit TOM20 homolog
N: Mitochondrial import receptor subunit TOM20 homolog


Theoretical massNumber of molelcules
Total (without water)32,6402
Polymers32,6402
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15060 Å2

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Components

#1: Protein Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 16319.862 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM20, KIAA0016 / Production host: Homo sapiens (human) / References: UniProt: Q15388

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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: The translocase of the outer mitochondrial membrane of Tom20 subunit
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: Digitonin
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347600 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0081438
ELECTRON MICROSCOPYf_angle_d1.3711956
ELECTRON MICROSCOPYf_dihedral_angle_d9.291186
ELECTRON MICROSCOPYf_chiral_restr0.061236
ELECTRON MICROSCOPYf_plane_restr0.011260

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