[English] 日本語
Yorodumi
- PDB-6ucv: Cryo-EM structure of the mitochondrial TOM complex from yeast (te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ucv
TitleCryo-EM structure of the mitochondrial TOM complex from yeast (tetramer)
Components(Mitochondrial import receptor subunit ...) x 5
KeywordsTRANSLOCASE / Membrane protein / mitochondrial protein import / mitochondrial outer membrane / protein translocation
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein transmembrane transport / protein import into mitochondrial matrix / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport ...mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein transmembrane transport / protein import into mitochondrial matrix / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol
Similarity search - Function
Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase ...Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit TOM6 / Mitochondrial import receptor subunit TOM22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit TOM5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPark, E. / Tucker, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1752814 United States
The Vallee Foundation United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution.
Authors: Kyle Tucker / Eunyong Park /
Abstract: Nearly all mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria after synthesis on cytosolic ribosomes. These precursor proteins are translocated into mitochondria ...Nearly all mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria after synthesis on cytosolic ribosomes. These precursor proteins are translocated into mitochondria by the TOM complex, a protein-conducting channel in the mitochondrial outer membrane. We have determined high-resolution cryo-EM structures of the core TOM complex from Saccharomyces cerevisiae in dimeric and tetrameric forms. Dimeric TOM consists of two copies each of five proteins arranged in two-fold symmetry: pore-forming β-barrel protein Tom40 and four auxiliary α-helical transmembrane proteins. The pore of each Tom40 has an overall negatively charged inner surface attributed to multiple functionally important acidic patches. The tetrameric complex is essentially a dimer of dimeric TOM, which may be capable of forming higher-order oligomers. Our study reveals the detailed molecular organization of the TOM complex and provides new insights about the mechanism of protein translocation into mitochondria.
History
DepositionSep 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20729
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial import receptor subunit TOM40
B: Mitochondrial import receptor subunit TOM22
C: Mitochondrial import receptor subunit TOM5
D: Mitochondrial import receptor subunit TOM6
E: Mitochondrial import receptor subunit TOM7
I: Mitochondrial import receptor subunit TOM40
J: Mitochondrial import receptor subunit TOM22
K: Mitochondrial import receptor subunit TOM5
L: Mitochondrial import receptor subunit TOM6
M: Mitochondrial import receptor subunit TOM7
a: Mitochondrial import receptor subunit TOM40
b: Mitochondrial import receptor subunit TOM22
c: Mitochondrial import receptor subunit TOM5
d: Mitochondrial import receptor subunit TOM6
e: Mitochondrial import receptor subunit TOM7
i: Mitochondrial import receptor subunit TOM40
j: Mitochondrial import receptor subunit TOM22
k: Mitochondrial import receptor subunit TOM5
l: Mitochondrial import receptor subunit TOM6
m: Mitochondrial import receptor subunit TOM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,47322
Polymers322,11820
Non-polymers1,3562
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Mitochondrial import receptor subunit ... , 5 types, 20 molecules AIaiBJbjCKckDLdlEMem

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


Mass: 43227.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P23644
#2: Protein
Mitochondrial import receptor subunit TOM22 / Mitochondrial 17 kDa assembly protein / Mitochondrial 22 kDa outer membrane protein / Protein MAS17 ...Mitochondrial 17 kDa assembly protein / Mitochondrial 22 kDa outer membrane protein / Protein MAS17 / Translocase of outer membrane 22 kDa subunit


Mass: 18020.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P49334
#3: Protein/peptide
Mitochondrial import receptor subunit TOM5 / Translocase of outer membrane 5 kDa subunit


Mass: 5993.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TOM5, MOM8A, YPR133W-A
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P80967
#4: Protein
Mitochondrial import receptor subunit TOM6 / Mitochondrial import site protein ISP6 / Translocase of outer membrane 6 kDa subunit


Mass: 6410.460 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TOM6, ISP6, YOR045W
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P33448
#5: Protein
Mitochondrial import receptor subunit TOM7 / Translocase of outer membrane 7 kDa subunit


Mass: 6876.955 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TOM7, MOM7, YNL070W, N2378
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P53507

-
Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H72NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tetrameric TOM complex from yeast / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (recombinant)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1Warp1.0.6particle selection
2SerialEM3.7image acquisition
4RELION2CTF correction
11cryoSPARC2.8.0final Euler assignment
13cryoSPARC2.8.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104905 / 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