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- EMDB-20729: Cryo-EM structure of the mitochondrial TOM complex from yeast (te... -

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Basic information

Entry
Database: EMDB / ID: EMD-20729
TitleCryo-EM structure of the mitochondrial TOM complex from yeast (tetramer)
Map dataFiltered, sharpened map
Sample
  • Complex: Tetrameric TOM complex from yeast
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
KeywordsMembrane protein / mitochondrial protein import / mitochondrial outer membrane / protein translocation / TRANSLOCASE
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport ...mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / 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 outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family ...Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
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 (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPark E / Tucker K
Funding support United States, 2 items
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, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseNov 6, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ucv
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20729.png

Downloads & links

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Map

FileDownload / File: emd_20729.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered, sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 400 pix.
= 460. Å		1.15 Å/pix.
x 400 pix.
= 460. Å		1.15 Å/pix.
x 400 pix.
= 460. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28 / Movie #1: 0.28
Minimum - Maximum-0.30605847 - 0.85899806
Average (Standard dev.)0.0009861945 (±0.024365356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 460.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z460.000460.000460.000
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3060.8590.001

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Supplemental data

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Additional map: Raw combined map

Fileemd_20729_additional.map
AnnotationRaw combined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric TOM complex from yeast

EntireName: Tetrameric TOM complex from yeast
Components
  • Complex: Tetrameric TOM complex from yeast
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Tetrameric TOM complex from yeast

SupramoleculeName: Tetrameric TOM complex from yeast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Macromolecule #1: Mitochondrial import receptor subunit TOM40

MacromoleculeName: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 43.227387 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString: MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE ...String:
MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE QDYQASDFSV NVKTLNPSFS EKGEFTGVAV ASFLQSVTPQ LALGLETLYS RTDGSAPGDA GVSYLTRYVS KK QDWIFSG QLQANGALIA SLWRKVAQNV EAGIETTLQA GMVPITDPLM GTPIGIQPTV EGSTTIGAKY EYRQSVYRGT LDS NGKVAC FLERKVLPTL SVLFCGEIDH FKNDTKIGCG LQFETAGNQE LLMLQQGLDA DGNPLQALPQ LGGWSHPQFE K

UniProtKB: Mitochondrial import receptor subunit TOM40

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Macromolecule #2: Mitochondrial import receptor subunit TOM22

MacromoleculeName: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 18.02065 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString:
MVELTEIKDD VVQLDEPQFS RNQAIVEEKA SATNNDVVDD EDDSDSDFED EFDENETLLD RIVALKDIVP PGKRQTISNF FGFTSSFVR NAFTKSGNLA WTLTTTALLL GVPLSLSILA EQQLIEMEKT FDLQSDANNI LAQGEKDAAA TANGGHHHHH H HH

UniProtKB: Mitochondrial import receptor subunit TOM22

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Macromolecule #3: Mitochondrial import receptor subunit TOM5

MacromoleculeName: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.993924 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString:
MFGLPQQEVS EEEKRAHQEQ TEKTLKQAAY VAAFLWVSPM IWHLVKKQWK

UniProtKB: Mitochondrial import receptor subunit TOM5

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Macromolecule #4: Mitochondrial import receptor subunit TOM6

MacromoleculeName: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 6.41046 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString:
MDGMFAMPGA AAGAASPQQP KSRFQAFKES PLYTIALNGA FFVAGVAFIQ SPLMDMLAPQ L

UniProtKB: Mitochondrial import receptor subunit TOM6

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Macromolecule #5: Mitochondrial import receptor subunit TOM7

MacromoleculeName: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 6.876955 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString:
MSFLPSFILS DESKERISKI LTLTHNVAHY GWIPFVLYLG WAHTSNRPNF LNLLSPLPSV

UniProtKB: Mitochondrial import receptor subunit TOM7

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Macromolecule #6: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: MC3
Molecular weightTheoretical: 677.933 Da
Chemical component information

ChemComp-MC3:
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: De novo model by CryoSPARC2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.8.0) / Number images used: 104905
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.8.0)
FSC plot (resolution estimation)

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