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- PDB-7cp9: Cryo-EM structure of human mitochondrial translocase TOM complex ... -

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Basic information

Entry
Database: PDB / ID: 7cp9
TitleCryo-EM structure of human mitochondrial translocase TOM complex at 3.0 angstrom.
Components(Mitochondrial import receptor subunit ...) x 5
KeywordsTRANSLOCASE / human mitochondrial translocase TOM complex / Outer membrane
Function / homology
Function and homology information


TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of type 2 mitophagy / Mitochondrial protein import / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / porin activity ...TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of type 2 mitophagy / Mitochondrial protein import / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / membrane / cytosol
Similarity search - Function
Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 ...Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Mitochondrial import receptor subunit TOM40 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: 3 Å
AuthorsGuan, Z. / Yan, L. / Wang, Q. / Yan, C. / Yin, P.
CitationJournal: Cell Discov / Year: 2021
Title: Structural insights into assembly of human mitochondrial translocase TOM complex.
Authors: Zeyuan Guan / Ling Yan / Qiang Wang / Liangbo Qi / Sixing Hong / Zhou Gong / Chuangye Yan / Ping Yin /
History
DepositionAug 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)156,23021
Polymers147,53810
Non-polymers8,69211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "D"
d_1ens_2chain "E"
d_2ens_2chain "F"
d_1ens_3chain "H"
d_2ens_3chain "G"
d_1ens_4chain "J"
d_2ens_4chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNSERC1 - 49
d_21ens_1ASNSERD1 - 49
d_11ens_2LEUGLYE1 - 52
d_21ens_2LEUGLYF1 - 52
d_11ens_3GLUGLNH1 - 86
d_21ens_3GLUGLNG1 - 86
d_11ens_4CYSGLYJ1 - 286
d_21ens_4CYSGLYI1 - 286

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.998659567745, -0.0503710420734, -0.0119090668218), (0.0498819902996, -0.998020245506, 0.0383063520014), (-0.0138150206616, 0.0376609569759, 0.99919507481)124.220929643, 134.434124808, -0.676234147355
2given(-0.999929637583, -0.00982547320245, 0.00664680064596), (0.00988699931261, -0.999907987285, 0.00928785272081), (0.00655493150777, 0.00935291611846, 0.999934775789)121.977589903, 139.310003927, -0.701822427271
3given(-0.999856222127, 0.0166917470536, -0.00298674656644), (-0.0167343029826, -0.999749825336, 0.0148408168457), (-0.00273828019727, 0.0148886641866, 0.999885408185)120.258328834, 140.272604125, -1.09530847945
4given(-0.999999986149, 0.000129814468967, -0.000104161188172), (-0.000129941766397, -0.999999243638, 0.00122304496008), (-0.000104002340456, 0.00122305847803, 0.999999246655)121.641134086, 139.93138466, -0.0826881161002

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Components

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Mitochondrial import receptor subunit ... , 5 types, 10 molecules ABCDEFGHIJ

#1: 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 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8N4H5
#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 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 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9P0U1
#4: 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): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NS69
#5: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM40, C19orf1, PEREC1, TOM40 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O96008

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Non-polymers , 1 types, 11 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY

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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 translocase / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 440 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenConc.: 10 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18rc6_3830refinement
PHENIX1.18rc6_3830refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
10RELION3initial Euler assignment
11RELION3final Euler assignment
12cryoSPARC2.15.0classification
13cryoSPARC2.15.03D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 360445 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 68.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00528687
ELECTRON MICROSCOPYf_angle_d0.640411640
ELECTRON MICROSCOPYf_chiral_restr0.0421241
ELECTRON MICROSCOPYf_plane_restr0.00451431
ELECTRON MICROSCOPYf_dihedral_angle_d21.73273502
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints3.5613E-13
ens_2d_2EELECTRON MICROSCOPYNCS constraints9.0728E-14
ens_3d_2HELECTRON MICROSCOPYNCS constraints1.6705E-12
ens_4d_2JELECTRON MICROSCOPYNCS constraints2.0866E-13

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