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- PDB-6lo8: Cryo-EM structure of the TIM22 complex from yeast -

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Basic information

Entry
Database: PDB / ID: 6lo8
TitleCryo-EM structure of the TIM22 complex from yeast
Components
  • (Mitochondrial import inner membrane translocase subunit ...) x 6
  • Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
KeywordsPROTEIN TRANSPORT / mitochondrial import / Tim22 / protein translocation / membrane protein insertion
Function / homology
Function and homology information


Glycerophospholipid biosynthesis / mitochondrial intermembrane space chaperone complex / Citric acid cycle (TCA cycle) / Sphingolipid de novo biosynthesis / Mitochondrial protein import / TIM22 mitochondrial import inner membrane insertion complex / mitochondrion targeting sequence binding / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / protein transporter activity ...Glycerophospholipid biosynthesis / mitochondrial intermembrane space chaperone complex / Citric acid cycle (TCA cycle) / Sphingolipid de novo biosynthesis / Mitochondrial protein import / TIM22 mitochondrial import inner membrane insertion complex / mitochondrion targeting sequence binding / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / protein transporter activity / protein transmembrane transport / protein insertion into mitochondrial inner membrane / cellular respiration / response to arsenic-containing substance / response to osmotic stress / protein transmembrane transporter activity / quinone binding / tricarboxylic acid cycle / phospholipid binding / mitochondrial intermembrane space / unfolded protein binding / cellular response to oxidative stress / electron transfer activity / mitochondrial inner membrane / intracellular membrane-bounded organelle / apoptotic process / structural molecule activity / mitochondrion / metal ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim54 / Inner membrane protein import complex subunit Tim54 / Mitochondrial import inner membrane translocase subunit tim13 like domains / : / : / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Mitochondrial import inner membrane translocase subunit TIM22 / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS ...Mitochondrial import inner membrane translocase subunit Tim54 / Inner membrane protein import complex subunit Tim54 / Mitochondrial import inner membrane translocase subunit tim13 like domains / : / : / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Mitochondrial import inner membrane translocase subunit TIM22 / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Tim17/Tim22/Tim23/Pmp24 family / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit TIM9 / Mitochondrial import inner membrane translocase subunit TIM12 / Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial / Mitochondrial import inner membrane translocase subunit TIM54 / Mitochondrial import inner membrane translocase subunit TIM10 / Mitochondrial import inner membrane translocase subunit TIM18 / Mitochondrial import inner membrane translocase subunit TIM22
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsZhang, Y. / Zhou, X. / Wu, X. / Li, L.
CitationJournal: Cell Res / Year: 2021
Title: Structure of the mitochondrial TIM22 complex from yeast.
Authors: Yutong Zhang / Xiaomin Ou / Xuezheng Wang / Dongjie Sun / Xueyin Zhou / Xiaofei Wu / Qing Li / Long Li /
History
DepositionJan 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

Deposited unit
A: Mitochondrial import inner membrane translocase subunit TIM22
B: Mitochondrial import inner membrane translocase subunit TIM54
C: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
D: Mitochondrial import inner membrane translocase subunit TIM18
E: Mitochondrial import inner membrane translocase subunit TIM9
F: Mitochondrial import inner membrane translocase subunit TIM12
G: Mitochondrial import inner membrane translocase subunit TIM9
H: Mitochondrial import inner membrane translocase subunit TIM10
I: Mitochondrial import inner membrane translocase subunit TIM9
J: Mitochondrial import inner membrane translocase subunit TIM10


Theoretical massNumber of molelcules
Total (without water)183,67110
Polymers183,67110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27790 Å2
ΔGint-186 kcal/mol
Surface area54930 Å2

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Components

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Mitochondrial import inner membrane translocase subunit ... , 6 types, 9 molecules ABDEGIFHJ

#1: Protein Mitochondrial import inner membrane translocase subunit TIM22


Mass: 21751.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12328
#2: Protein Mitochondrial import inner membrane translocase subunit TIM54


Mass: 54252.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47045
#4: Protein Mitochondrial import inner membrane translocase subunit TIM18


Mass: 21994.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08749
#5: Protein Mitochondrial import inner membrane translocase subunit TIM9


Mass: 10216.649 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O74700
#6: Protein Mitochondrial import inner membrane translocase subunit TIM12 / Mitochondrial regulator of splicing 5


Mass: 12299.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32830
#7: Protein Mitochondrial import inner membrane translocase subunit TIM10 / Mitochondrial intermembrane protein MRS11


Mass: 10313.589 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P87108

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Protein , 1 types, 1 molecules C

#3: Protein Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial


Mass: 22094.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33421

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Details

Has protein modificationY

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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: TIM22 complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5465
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 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
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 57 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_refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3663107
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251984 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 93.66 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00498117
ELECTRON MICROSCOPYf_angle_d0.857910903
ELECTRON MICROSCOPYf_chiral_restr0.04931185
ELECTRON MICROSCOPYf_plane_restr0.00751392
ELECTRON MICROSCOPYf_dihedral_angle_d16.64593029

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