7BTY

The mitochondrial SAM-Mdm10 supercomplex in Nanodisc from S.cere


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mitochondrial sorting and assembly machinery operates by beta-barrel switching.

Takeda, H.Tsutsumi, A.Nishizawa, T.Lindau, C.Busto, J.V.Wenz, L.S.Ellenrieder, L.Imai, K.Straub, S.P.Mossmann, W.Qiu, J.Yamamori, Y.Tomii, K.Suzuki, J.Murata, T.Ogasawara, S.Nureki, O.Becker, T.Pfanner, N.Wiedemann, N.Kikkawa, M.Endo, T.

(2021) Nature 590: 163-169

  • DOI: https://doi.org/10.1038/s41586-020-03113-7
  • Primary Citation of Related Structures:  
    7BTW, 7BTX, 7BTY

  • PubMed Abstract: 

    The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior 1-3 . Insertion of β-barrel proteins into the outer membrane is mediated by the multisubunit mitochondrial sorting and assembly machinery (SAM, also known as TOB) 4-6 . 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.


  • Organizational Affiliation

    Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial outer membrane beta-barrel protein363Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E9P977 (Saccharomyces cerevisiae)
Explore E9P977 
Go to UniProtKB:  E9P977
Entity Groups  
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UniProt GroupE9P977
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting assembly machinery 35 kDa subunit329Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14693 
Go to UniProtKB:  P14693
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UniProt GroupP14693
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting assembly machinery 37 kDa subunit327Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P50110 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50110 
Go to UniProtKB:  P50110
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UniProt GroupP50110
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MDM10 isoform 1D [auth L]493Saccharomyces cerevisiaeMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)--
Japan Science and Technology--
Japan Agency for Medical Research and Development (AMED)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references