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- PDB-7bty: The mitochondrial SAM-Mdm10 supercomplex in Nanodisc from S.cere -

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Basic information

Entry
Database: PDB / ID: 7bty
TitleThe mitochondrial SAM-Mdm10 supercomplex in Nanodisc from S.cere
Components
  • MDM10 isoform 1
  • Mitochondrial outer membrane beta-barrel protein
  • Sorting assembly machinery 35 kDa subunit
  • Sorting assembly machinery 37 kDa subunit
KeywordsTRANSLOCASE / Mitochondria
Function / homology
Function and homology information


ERMES complex / SAM complex / mitochondrial outer membrane translocase complex assembly / phospholipid transport / outer membrane / protein insertion into mitochondrial outer membrane / mitochondrion organization / mitochondrial outer membrane / mitochondrion / integral component of membrane / cytoplasm
Surface antigen D15-like / Tom37, C-terminal domain / Mitochondrial distribution and morphology protein 10 / Sorting assembly machinery 35kDa subunit / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Bacterial surface antigen (D15)
MDM10 isoform 1 / Mitochondrial outer membrane beta-barrel protein / Sorting assembly machinery 35 kDa subunit / Sorting assembly machinery 37 kDa subunit
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTakeda, H. / Tsutsumi, A. / Nishizawa, T. / Nureki, O. / Kikkawa, M. / Endo, T.
Funding support3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)
Japan Science and Technology
Japan Agency for Medical Research and Development (AMED)
CitationJournal: Nature / Year: 2021
Title: Mitochondrial sorting and assembly machinery operates by β-barrel switching.
Authors: Hironori Takeda / Akihisa Tsutsumi / Tomohiro Nishizawa / Caroline Lindau / Jon V Busto / Lena-Sophie Wenz / Lars Ellenrieder / Kenichiro Imai / Sebastian P Straub / Waltraut Mossmann / Jian ...Authors: Hironori Takeda / Akihisa Tsutsumi / Tomohiro Nishizawa / Caroline Lindau / Jon V Busto / Lena-Sophie Wenz / Lars Ellenrieder / Kenichiro Imai / Sebastian P Straub / Waltraut Mossmann / Jian Qiu / Yu Yamamori / Kentaro Tomii / Junko Suzuki / Takeshi Murata / Satoshi Ogasawara / Osamu Nureki / Thomas Becker / Nikolaus Pfanner / Nils Wiedemann / Masahide Kikkawa / Toshiya Endo /
Abstract: The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior. Insertion of β-barrel proteins into the outer ...The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior. Insertion of β-barrel proteins into the outer membrane is mediated by the multisubunit mitochondrial sorting and assembly machinery (SAM, also known as TOB). Here we use cryo-electron microscopy to determine the structures of two different forms of the yeast SAM complex at a resolution of 2.8-3.2 Å. The dimeric complex contains two copies of the β-barrel channel protein Sam50-Sam50a and Sam50b-with partially open lateral gates. The peripheral membrane proteins Sam35 and Sam37 cap the Sam50 channels from the cytosolic side, and are crucial for the structural and functional integrity of the dimeric complex. In the second complex, Sam50b is replaced by the β-barrel protein Mdm10. In cooperation with Sam50a, Sam37 recruits and traps Mdm10 by penetrating the interior of its laterally closed β-barrel from the cytosolic side. The substrate-loaded SAM complex contains one each of Sam50, Sam35 and Sam37, but neither Mdm10 nor a second Sam50, suggesting that Mdm10 and Sam50b function as placeholders for a β-barrel substrate released from Sam50a. Our proposed mechanism for dynamic switching of β-barrel subunits and substrate explains how entire precursor proteins can fold in association with the mitochondrial machinery for β-barrel assembly.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 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_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Mitochondrial outer membrane beta-barrel protein
B: Sorting assembly machinery 35 kDa subunit
C: Sorting assembly machinery 37 kDa subunit
L: MDM10 isoform 1


Theoretical massNumber of molelcules
Total (without water)172,4574
Polymers172,4574
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10830 Å2
ΔGint-58 kcal/mol
Surface area57800 Å2

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Components

#1: Protein Mitochondrial outer membrane beta-barrel protein / SAM50 isoform 1


Mass: 41176.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: E9P977
#2: Protein Sorting assembly machinery 35 kDa subunit / Sam35


Mass: 37446.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14693
#3: Protein Sorting assembly machinery 37 kDa subunit / Sam37


Mass: 37537.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P50110
#4: Protein MDM10 isoform 1


Mass: 56296.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A0A6A5PXD8

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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: SAM-Mdm10 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 299 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 FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1.13CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128400 / Symmetry type: POINT

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