[English] 日本語
Yorodumi
- EMDB-15849: Cryo-EM structure of the Neurospora crassa TOM core complex at 3.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15849
TitleCryo-EM structure of the Neurospora crassa TOM core complex at 3.3 angstrom
Map dataSharpened cryoEM map used for model building.
Sample
  • Complex: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
    • Complex: Mitochondrial import receptor subunit Tom22
      • Protein or peptide: Mitochondrial import receptor subunit Tom22
    • Complex: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
      • Protein or peptide: Mitochondrial import receptor subunit Tom40
      • Protein or peptide: Translocase of outer mitochondrial membrane subunit 5
      • Protein or peptide: TOM6
      • Protein or peptide: TOM7
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
KeywordsComplex / outer membrane / mitochondria / membrane protein / TOM / translocase / neurospora crassa
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein targeting to mitochondrion / porin activity / pore complex / protein transmembrane transporter activity / mitochondrial outer membrane
Similarity search - Function
Mitochondrial import receptor subunit Tom22, fungi / 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 ...Mitochondrial import receptor subunit Tom22, fungi / 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
Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit tom22 / Translocase of outer mitochondrial membrane subunit 5 / TOM7 / TOM6
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsOrnelas P / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Two conformations of the Tom20 preprotein receptor in the TOM holo complex.
Authors: Pamela Ornelas / Thomas Bausewein / Janosch Martin / Nina Morgner / Stephan Nussberger / Werner Kühlbrandt /
Abstract: The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into ...The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into mitochondria. We have determined the structure of the TOM core complex from by single-particle electron cryomicroscopy at 3.3 Å resolution, showing its interaction with a bound preprotein at 4 Å resolution, and of the TOM holo complex including the Tom20 receptor at 6 to 7 Å resolution. TOM is a transmembrane complex consisting of two β-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 has a transmembrane helix and a receptor domain on the cytoplasmic side. We propose that Tom20 acts as a dynamic gatekeeper, guiding preproteins into the pores of the TOM complex. We analyze the interactions of Tom20 with other TOM subunits, present insights into the structure of the TOM holo complex, and suggest a translocation mechanism.
History
DepositionSep 20, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15849.png

Downloads & links

-
Map

FileDownload / File: emd_15849.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryoEM map used for model building.
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.167
Minimum - Maximum-0.45550093 - 0.8340952
Average (Standard dev.)0.00092189317 (±0.016739497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 321.40802 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15849_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Refinement map without postprocessing.

Fileemd_15849_additional_1.map
AnnotationRefinement map without postprocessing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_15849_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_15849_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Translocase of the outer mitochondrial membrane core complex of N...

EntireName: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
Components
  • Complex: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
    • Complex: Mitochondrial import receptor subunit Tom22
      • Protein or peptide: Mitochondrial import receptor subunit Tom22
    • Complex: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
      • Protein or peptide: Mitochondrial import receptor subunit Tom40
      • Protein or peptide: Translocase of outer mitochondrial membrane subunit 5
      • Protein or peptide: TOM6
      • Protein or peptide: TOM7
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

+
Supramolecule #1: Translocase of the outer mitochondrial membrane core complex of N...

SupramoleculeName: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

+
Supramolecule #2: Mitochondrial import receptor subunit Tom22

SupramoleculeName: Mitochondrial import receptor subunit Tom22 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Neurospora crassa (fungus)

+
Supramolecule #3: Translocase of the outer mitochondrial membrane core complex of N...

SupramoleculeName: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3-#5
Source (natural)Organism: Neurospora crassa (fungus) / Strain: GR-107 / Organelle: Mitochondria

+
Macromolecule #1: Mitochondrial import receptor subunit Tom40

MacromoleculeName: Mitochondrial import receptor subunit Tom40 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 38.184797 KDa
SequenceString: MASFSTESPL AMLRDNAIYS SLSDAFNAFQ ERRKQFGLSN PGTIETIARE VQRDTLLTNY MFSGLRADVT KAFSLAPLFQ VSHQFAMGE RLNPYAFAAL YGTNQIFAQG NLDNEGALST RFNYRWGDRT ITKTQFSIGG GQDMAQFEHE HLGDDFSASL K AINPSFLD ...String:
MASFSTESPL AMLRDNAIYS SLSDAFNAFQ ERRKQFGLSN PGTIETIARE VQRDTLLTNY MFSGLRADVT KAFSLAPLFQ VSHQFAMGE RLNPYAFAAL YGTNQIFAQG NLDNEGALST RFNYRWGDRT ITKTQFSIGG GQDMAQFEHE HLGDDFSASL K AINPSFLD GGLTGIFVGD YLQAVTPRLG LGLQAVWQRQ GLTQGPDTAI SYFARYKAGD WVASAQLQAQ GALNTSFWKK LT DRVQAGV DMTLSVAPSQ SMMGGLTKEG ITTFGAKYDF RMSTFRAQID SKGKLSCLLE KRLGAAPVTL TFAADVDHVT QQA KLGMSV SIEASDVDLQ EQQEGAQSLN IPF

UniProtKB: Mitochondrial import receptor subunit TOM40

+
Macromolecule #2: Mitochondrial import receptor subunit Tom22

MacromoleculeName: Mitochondrial import receptor subunit Tom22 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 17.657141 KDa
Recombinant expressionOrganism: Neurospora crassa (fungus)
SequenceString:
MVQLTEVEDE HFQQPQVGPE EDDEDFTDTD SEISVDSDYE SQETFTDRLY ALRDMVSPTT RGWFYHKYST TTNFVKSTLS FAGRAAWAV SVSGLLIGVP FAIAFAEDQN YAAMEQEARM RELGSDVLTA GGEGQAGTAE KTLAAIGGEG ARPALHHHHH H

UniProtKB: Mitochondrial import receptor subunit tom22

+
Macromolecule #3: Translocase of outer mitochondrial membrane subunit 5

MacromoleculeName: Translocase of outer mitochondrial membrane subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 5.4052 KDa
SequenceString:
MFGGFQPPAL SREELQAAEA EATFTIQRAV FTAVALYLSP FVIDAVSKVL

UniProtKB: Translocase of outer mitochondrial membrane subunit 5

+
Macromolecule #4: TOM6

MacromoleculeName: TOM6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 6.470329 KDa
SequenceString:
MPSAKYIERP GGSRKSKGFI RSTYDSLTSS ENASVVRSIA FFGAAVAFLS SSWGEMLVVQ

UniProtKB: TOM6

+
Macromolecule #5: TOM7

MacromoleculeName: TOM7 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 6.069213 KDa
SequenceString:
MFALSEESKE RIGKLIDISR VVVHYGYLPL ILYLGYTRSV PRPSIIRLLS PLS

UniProtKB: TOM7

+
Macromolecule #6: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13...

MacromoleculeName: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
type: ligand / ID: 6 / Number of copies: 8 / Formula: DU0
Molecular weightTheoretical: 516.752 Da
Chemical component information

ChemComp-DU0:
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol

+
Macromolecule #7: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 306000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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