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- PDB-7e4i: Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 ... -

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Basic information

Entry
Database: PDB / ID: 7e4i
TitleCryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom
Components
  • (Mitochondrial import receptor subunit ...) x 3
  • (Sorting assembly machinery ...) x 3
KeywordsTRANSLOCASE
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex / mitochondrial respiratory chain complex assembly / protein import into mitochondrial matrix / phospholipid transport / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity ...mitochondrial outer membrane translocase complex assembly / SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex / mitochondrial respiratory chain complex assembly / protein import into mitochondrial matrix / phospholipid transport / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrion organization / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial outer membrane / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Outer mitochondrial membrane transport complex protein / Mitochondrial outer membrane translocase complex, subunit Tom5 ...Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Outer mitochondrial membrane transport complex protein / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin domain superfamily
Similarity search - Domain/homology
Sorting assembly machinery 35 kDa subunit / Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit TOM6 / Sorting assembly machinery 37 kDa subunit / Sorting assembly machinery 50 kDa subunit / Mitochondrial import receptor subunit TOM5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWang, Q. / Guan, Z.Y. / Qi, L.B. / Yan, C.Y. / Yin, P.
CitationJournal: Science / Year: 2021
Title: Structural insight into the SAM-mediated assembly of the mitochondrial TOM core complex.
Authors: Qiang Wang / Zeyuan Guan / Liangbo Qi / Jinjin Zhuang / Chen Wang / Sixing Hong / Ling Yan / Yan Wu / Xiaoqian Cao / Jianbo Cao / Junjie Yan / Tingting Zou / Zhu Liu / Delin Zhang / Chuangye Yan / Ping Yin /
Abstract: β barrel outer membrane proteins (β-OMPs) play vital roles in mitochondria, chloroplasts, and Gram-negative bacteria. Evolutionarily conserved complexes such as the mitochondrial sorting and ...β barrel outer membrane proteins (β-OMPs) play vital roles in mitochondria, chloroplasts, and Gram-negative bacteria. Evolutionarily conserved complexes such as the mitochondrial sorting and assembly machinery (SAM) mediate the assembly of β-OMPs. We investigated the SAM-mediated assembly of the translocase of the outer membrane (TOM) core complex. Cryo–electron microscopy structures of SAM–fully folded Tom40 and the SAM-Tom40/Tom5/Tom6 complexes at ~3-angstrom resolution reveal that Sam37 stabilizes the mature Tom40 mainly through electrostatic interactions, thus facilitating subsequent TOM assembly. These results support the β barrel switching model and provide structural insights into the assembly and release of β barrel complexes.
History
DepositionFeb 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Sorting assembly machinery 50 kDa subunit
B: Sorting assembly machinery 35 kDa subunit
C: Sorting assembly machinery 37 kDa subunit
D: Mitochondrial import receptor subunit TOM40
E: Mitochondrial import receptor subunit TOM5
F: Mitochondrial import receptor subunit TOM6


Theoretical massNumber of molelcules
Total (without water)189,1156
Polymers189,1156
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11890 Å2
ΔGint-85 kcal/mol
Surface area72950 Å2

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Components

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Sorting assembly machinery ... , 3 types, 3 molecules ABC

#1: Protein Sorting assembly machinery 50 kDa subunit / TOB complex 55 kDa subunit


Mass: 54544.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SAM50, TOB55, YNL026W, N2802 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P53969
#2: Protein Sorting assembly machinery 35 kDa subunit / Mitochondrial 38 kDa outer membrane protein / TOB complex 38 kDa subunit


Mass: 37446.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SAM35, OMP85, TOB38, TOM38, YHR083W / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P14693
#3: Protein Sorting assembly machinery 37 kDa subunit / MAS37 protein / Mitochondrial 37 kDa outer membrane protein


Mass: 40498.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SAM37, MAS37, PET3027, TOM37, YMR060C, YM9796.13C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P50110

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Mitochondrial import receptor subunit ... , 3 types, 3 molecules DEF

#4: Protein Mitochondrial import receptor subunit TOM40 / Mitochondrial import site protein ISP42 / Translocase of outer membrane 40 kDa subunit


Mass: 43947.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P23644
#5: Protein Mitochondrial import receptor subunit TOM5 / Translocase of outer membrane 5 kDa subunit


Mass: 6196.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM5, MOM8A, YPR133W-A / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P80967
#6: Protein Mitochondrial import receptor subunit TOM6 / Mitochondrial import site protein ISP6 / Translocase of outer membrane 6 kDa subunit


Mass: 6481.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM6, ISP6, YOR045W / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P33448

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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

Component
IDNameTypeEntity IDParent-IDSource
1SAM-Tom40/Tom5/Tom6 complexCOMPLEXall0RECOMBINANT
2Sorting assembly machinery subunitsCOMPLEX#1-#31RECOMBINANT
3Mitochondrial import receptor subunitsCOMPLEX#4-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae S288c (yeast)559292
32Saccharomyces cerevisiae S288c (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293
32Homo sapiens (human)9606HEK293
Buffer solutionpH: 7.4
SpecimenConc.: 6 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
11cryoSPARC3final Euler assignment
13cryoSPARC33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 406531 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211565
ELECTRON MICROSCOPYf_angle_d0.4615631
ELECTRON MICROSCOPYf_dihedral_angle_d9.94248
ELECTRON MICROSCOPYf_chiral_restr0.0391764
ELECTRON MICROSCOPYf_plane_restr0.0031988

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