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- PDB-7vby: Tom core complex with Tom20 and Tom22 subunits. -

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Basic information

Entry
Database: PDB / ID: 7vby
TitleTom core complex with Tom20 and Tom22 subunits.
Components
  • (Mitochondrial import receptor subunit ...) x 4
  • Translocase of the Outer Membrane
KeywordsTRANSLOCASE / Tom complex / Tom20 / Cryo-EM
Function / homology
Function and homology information


TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / positive regulation of type 2 mitophagy / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity ...TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / positive regulation of type 2 mitophagy / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / mitochondrial outer membrane / mitochondrion / membrane
Similarity search - Function
Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / 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
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / UNDECANE / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 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: Tom core complex with Tom20 and Tom22 subunits.
Authors: Liu, D.S. / Sui, S.F.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Translocase of the Outer Membrane
A: Mitochondrial import receptor subunit TOM6 homolog
D: Mitochondrial import receptor subunit TOM5 homolog
F: Mitochondrial import receptor subunit TOM6 homolog
G: Mitochondrial import receptor subunit TOM7 homolog
E: Mitochondrial import receptor subunit TOM5 homolog
I: Translocase of the Outer Membrane
H: Mitochondrial import receptor subunit TOM22 homolog
C: Mitochondrial import receptor subunit TOM22 homolog
J: Mitochondrial import receptor subunit TOM7 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,25033
Polymers251,68310
Non-polymers10,56723
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, gel filtration, gel filtration, gel filtration, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35800 Å2
ΔGint-233 kcal/mol
Surface area55520 Å2

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Components

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Protein , 1 types, 2 molecules BI

#1: Protein Translocase of the Outer Membrane


Mass: 89999.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Mitochondrial import receptor subunit ... , 4 types, 8 molecules AFDEGJHC

#2: Protein Mitochondrial import receptor subunit TOM6 homolog / Overexpressed breast tumor protein / Translocase of outer membrane 6 kDa subunit homolog


Mass: 8007.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM6, OBTP, TOM6 / Production host: Homo sapiens (human) / References: UniProt: Q96B49
#3: Protein Mitochondrial import receptor subunit TOM5 homolog


Mass: 6045.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM5, C9orf105, TOM5 / Production host: Homo sapiens (human) / References: UniProt: Q8N4H5
#4: Protein Mitochondrial import receptor subunit TOM7 homolog / Translocase of outer membrane 7 kDa subunit homolog


Mass: 6256.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM7, TOM7, TOMM07, AD-014 / Production host: Homo sapiens (human) / References: UniProt: Q9P0U1
#5: Protein Mitochondrial import receptor subunit TOM22 homolog / hTom22 / 1C9-2 / Translocase of outer membrane 22 kDa subunit homolog


Mass: 15532.528 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM22, TOM22 / Production host: Homo sapiens (human) / References: UniProt: Q9NS69

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Non-polymers , 2 types, 23 molecules

#6: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#7: Chemical
ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H24

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Tox complex / Type: COMPLEX / Entity ID: #1-#5 / 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: DIG
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 FIELD
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: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288736 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058494
ELECTRON MICROSCOPYf_angle_d0.59311403
ELECTRON MICROSCOPYf_dihedral_angle_d25.0811655
ELECTRON MICROSCOPYf_chiral_restr0.041257
ELECTRON MICROSCOPYf_plane_restr0.0041364

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