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- PDB-8xva: Human TOM complex with whole Tom20 -

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Basic information

Entry
Database: PDB / ID: 8xva
TitleHuman TOM complex with whole Tom20
Components(Mitochondrial import receptor subunit ...) x 6
KeywordsPROTEIN TRANSPORT / mitochondria / transport / membrane protein complex
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitophagy in response to mitochondrial depolarization / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import ...tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitophagy in response to mitochondrial depolarization / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / sperm midpiece / PINK1-PRKN Mediated Mitophagy / cell periphery / regulation of protein stability / unfolded protein binding / mitochondrial outer membrane / mitochondrial inner membrane / Ub-specific processing proteases / mitochondrion / membrane / cytosol
Similarity search - Function
Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 ...Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / 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 homolog / Mitochondrial import receptor subunit TOM20 homolog / 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: 5.92 Å
AuthorsTian, X.Y. / Su, J.Y. / Sui, S.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: PNAS Nexus / Year: 2024
Title: Structure of the intact Tom20 receptor in the human translocase of the outer membrane complex.
Authors: Jiayue Su / Xuyang Tian / Ziyi Wang / Jiawen Yang / Shan Sun / Sen-Fang Sui /
Abstract: The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor ...The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor proteins, featuring amino-terminal targeting signals (presequences) or internal targeting signals, are recognized by the TOM complex receptors Tom20, Tom22, and Tom70, and then translocated into mitochondria through Tom40. By using chemical cross-linking to stabilize Tom20 in the TOM complex, this study unveils the structure of the human TOM holo complex, encompassing the intact Tom20 component, at a resolution of approximately 6 Å by cryo-electron microscopy. Our structure shows the TOM holo complex containing only one Tom20 subunit, which is located right at the center of the complex and stabilized by extensive interactions with Tom22, Tom40, and Tom6. Based on the structure, we proposed a possible translocation mode of TOM complex, by which different receptors could work simultaneously to ensure that the preproteins recognized by them are all efficiently translocated into the mitochondria.
History
DepositionJan 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial import receptor subunit TOM6 homolog
B: Mitochondrial import receptor subunit TOM40 homolog
C: Mitochondrial import receptor subunit TOM22 homolog
D: Mitochondrial import receptor subunit TOM5 homolog
E: Mitochondrial import receptor subunit TOM5 homolog
F: Mitochondrial import receptor subunit TOM6 homolog
G: Mitochondrial import receptor subunit TOM7 homolog
H: Mitochondrial import receptor subunit TOM22 homolog
I: Mitochondrial import receptor subunit TOM40 homolog
J: Mitochondrial import receptor subunit TOM7 homolog
K: Mitochondrial import receptor subunit TOM20 homolog


Theoretical massNumber of molelcules
Total (without water)163,85811
Polymers163,85811
Non-polymers00
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

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Mitochondrial import receptor subunit ... , 6 types, 11 molecules AFBICHDEGJK

#1: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F / References: UniProt: Q96B49
#2: Protein Mitochondrial import receptor subunit TOM40 homolog / Protein Haymaker / Translocase of outer membrane 40 kDa subunit homolog / p38.5


Mass: 37926.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F / References: UniProt: O96008
#3: 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 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q9NS69
#4: Protein Mitochondrial import receptor subunit TOM5 homolog


Mass: 6045.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F / References: UniProt: Q8N4H5
#5: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0U1
#6: 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.: 1 / Source method: isolated from a natural source / Source: (natural) 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: TOM complex with whole Tom20 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 168.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F / Plasmid: 3X Flag-PCMV
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMOPSC7H15NO4S1
2150 mMpotassium chlorideKCl1
30.1 %DIGC56H92O291
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 K

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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 / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1151405
3D reconstructionResolution: 5.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189667 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058843
ELECTRON MICROSCOPYf_angle_d0.92111946
ELECTRON MICROSCOPYf_dihedral_angle_d25.2751181
ELECTRON MICROSCOPYf_chiral_restr0.0491336
ELECTRON MICROSCOPYf_plane_restr0.0051529

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