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- PDB-8xkx: Structure of the TOM40 complex with pre-protein -

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Basic information

Entry
Database: PDB / ID: 8xkx
TitleStructure of the TOM40 complex with pre-protein
Components
  • Mitochondrial import receptor subunit TOM22
  • Mitochondrial import receptor subunit TOM40
  • Mitochondrial import receptor subunit TOM5
  • Mitochondrial import receptor subunit TOM6
  • Mitochondrial import receptor subunit TOM7
KeywordsMEMBRANE PROTEIN / Mitochondrial precursor protein translocase / Mitochondrial pre-protein transporte / Protein complex / mitochondrial outer membrane protein
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity / monoatomic ion transport ...mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol
Similarity search - Function
Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase ...Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit TOM6 / Mitochondrial import receptor subunit TOM22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit TOM5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYang, L.Y. / Shen, Q.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the TOM40 complex with pre-protein
Authors: Yang, L.Y. / Shen, Q.T.
History
DepositionDec 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Mitochondrial import receptor subunit TOM22
C: Mitochondrial import receptor subunit TOM5
D: Mitochondrial import receptor subunit TOM6
E: Mitochondrial import receptor subunit TOM7
A: Mitochondrial import receptor subunit TOM40
G: Mitochondrial import receptor subunit TOM22
H: Mitochondrial import receptor subunit TOM5
I: Mitochondrial import receptor subunit TOM6
J: Mitochondrial import receptor subunit TOM7
F: Mitochondrial import receptor subunit TOM40


Theoretical massNumber of molelcules
Total (without water)161,09510
Polymers161,09510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mitochondrial import receptor subunit TOM22 / Mitochondrial 17 kDa assembly protein / Mitochondrial 22 kDa outer membrane protein / Protein MAS17 ...Mitochondrial 17 kDa assembly protein / Mitochondrial 22 kDa outer membrane protein / Protein MAS17 / Translocase of outer membrane 22 kDa subunit


Mass: 19194.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YPH499 / Gene: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862 / Variant: Tom22-10His / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49334
#2: Protein/peptide Mitochondrial import receptor subunit TOM5 / Translocase of outer membrane 5 kDa subunit


Mass: 5993.924 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499 / References: UniProt: P80967
#3: Protein Mitochondrial import receptor subunit TOM6 / Mitochondrial import site protein ISP6 / Translocase of outer membrane 6 kDa subunit


Mass: 6410.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499 / References: UniProt: P33448
#4: Protein Mitochondrial import receptor subunit TOM7 / Translocase of outer membrane 7 kDa subunit


Mass: 6876.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499 / References: UniProt: P53507
#5: Protein Mitochondrial import receptor subunit TOM40 / Mitochondrial import site protein ISP42 / Translocase of outer membrane 40 kDa subunit


Mass: 42071.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499 / References: UniProt: P23644
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: TOM40 complex with pre-protein / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: YPH499
Buffer solutionpH: 7.2
SpecimenConc.: 2 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027686
ELECTRON MICROSCOPYf_angle_d0.68310424
ELECTRON MICROSCOPYf_dihedral_angle_d4.9121012
ELECTRON MICROSCOPYf_chiral_restr0.0561174
ELECTRON MICROSCOPYf_plane_restr0.0031338

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