[English] 日本語
Yorodumi
- PDB-7btx: The mitochondrial SAM-Mdm10 supercomplex in GDN micelle from S.cere -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7btx
TitleThe mitochondrial SAM-Mdm10 supercomplex in GDN micelle 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 / protein insertion into mitochondrial outer membrane / outer membrane / phospholipid transport / protein import into mitochondrial matrix / mitochondrion organization / mitochondrial outer membrane / mitochondrion / cytoplasm
Similarity search - Function
Mitochondrial distribution and morphology protein 10 / Mitochondrial distribution and morphology protein 10 / Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / membrane protein fhac: a member of the omp85/tpsb transporter family ...Mitochondrial distribution and morphology protein 10 / Mitochondrial distribution and morphology protein 10 / Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / membrane protein fhac: a member of the omp85/tpsb transporter family / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MDM10 isoform 1 / Mitochondrial outer membrane beta-barrel protein / Sorting assembly machinery 35 kDa subunit / Sorting assembly machinery 37 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTakeda, H. / Tsutsumi, A. / Nishizawa, T. / Nureki, O. / Kikkawa, M. / Endo, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Science and Technology Japan
Japan Agency for Medical Research and Development (AMED) Japan
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.
History
DepositionApr 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 20, 2021Data content type: Primary map / Data content type: Primary map / Provider: 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
Revision 1.2Mar 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
Revision 1.3Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30190
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10410 Å2
ΔGint-60 kcal/mol
Surface area58800 Å2

-
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 (brewer'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 (brewer'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 (brewer'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 (brewer's yeast) / References: UniProt: A0A6A5PXD8
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: SAM-Mdm10 complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer'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

-
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 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1.13CTF correction
8PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186871 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more