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- EMDB-38694: Human TOM complex with whole Tom20 -

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Basic information

Entry
Database: EMDB / ID: EMD-38694
TitleHuman TOM complex with whole Tom20
Map data
Sample
  • Complex: TOM complex with whole Tom20
    • Protein or peptide: Mitochondrial import receptor subunit TOM6 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM40 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM22 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM5 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM7 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
Keywordsmitochondria / transport / membrane protein complex / PROTEIN TRANSPORT
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import ...tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import / positive regulation of type 2 mitophagy / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / porin activity / response to muscle activity / pore complex / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity / monoatomic ion transport / sperm midpiece / PINK1-PRKN Mediated Mitophagy / cell periphery / regulation of protein stability / unfolded protein binding / mitochondrial outer membrane / mitochondrial inner membrane / Ub-specific processing proteases / mitochondrion / membrane / cytosol
Similarity search - Function
Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 ...Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / 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 homolog / Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.92 Å
AuthorsTian XY / Su JY / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: PNAS Nexus / Year: 2024
Title: Structure of the intact Tom20 receptor in the human translocase of the outer membrane complex.
Authors: Jiayue Su / Xuyang Tian / Ziyi Wang / Jiawen Yang / Shan Sun / Sen-Fang Sui /
Abstract: The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor ...The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor proteins, featuring amino-terminal targeting signals (presequences) or internal targeting signals, are recognized by the TOM complex receptors Tom20, Tom22, and Tom70, and then translocated into mitochondria through Tom40. By using chemical cross-linking to stabilize Tom20 in the TOM complex, this study unveils the structure of the human TOM holo complex, encompassing the intact Tom20 component, at a resolution of approximately 6 Å by cryo-electron microscopy. Our structure shows the TOM holo complex containing only one Tom20 subunit, which is located right at the center of the complex and stabilized by extensive interactions with Tom22, Tom40, and Tom6. Based on the structure, we proposed a possible translocation mode of TOM complex, by which different receptors could work simultaneously to ensure that the preproteins recognized by them are all efficiently translocated into the mitochondria.
History
DepositionJan 14, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38694.png

Downloads & links

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Map

FileDownload / File: emd_38694.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 280 pix.
= 303.1 Å		1.08 Å/pix.
x 280 pix.
= 303.1 Å		1.08 Å/pix.
x 280 pix.
= 303.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.51
Minimum - Maximum-8.366770000000001 - 32.609580000000001
Average (Standard dev.)0.002339889 (±0.98157364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 303.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TOM complex with whole Tom20

EntireName: TOM complex with whole Tom20
Components
  • Complex: TOM complex with whole Tom20
    • Protein or peptide: Mitochondrial import receptor subunit TOM6 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM40 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM22 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM5 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM7 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog

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Supramolecule #1: TOM complex with whole Tom20

SupramoleculeName: TOM complex with whole Tom20 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 168.3 kDa/nm

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Macromolecule #1: Mitochondrial import receptor subunit TOM6 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM6 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.007988 KDa
SequenceString:
MASSTVPVSA AGSANETPEI PDNVGDWLRG VYRFATDRND FRRNLILNLG LFAAGVWLAR NLSDIDLMAP QPGV

UniProtKB: Mitochondrial import receptor subunit TOM6 homolog

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Macromolecule #2: Mitochondrial import receptor subunit TOM40 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM40 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.926926 KDa
SequenceString: MGNVLAASSP PAGPPPPPAP ALVGLPPPPP SPPGFTLPPL GGSLGAGTST SRSSERTPGA ATASASGAAE DGACGCLPNP GTFEECHRK CKELFPIQME GVKLTVNKGL SNHFQVNHTV ALSTIGESNY HFGVTYVGTK QLSPTEAFPV LVGDMDNSGS L NAQVIHQL ...String:
MGNVLAASSP PAGPPPPPAP ALVGLPPPPP SPPGFTLPPL GGSLGAGTST SRSSERTPGA ATASASGAAE DGACGCLPNP GTFEECHRK CKELFPIQME GVKLTVNKGL SNHFQVNHTV ALSTIGESNY HFGVTYVGTK QLSPTEAFPV LVGDMDNSGS L NAQVIHQL GPGLRSKMAI QTQQSKFVNW QVDGEYRGSD FTAAVTLGNP DVLVGSGILV AHYLQSITPC LALGGELVYH RR PGEEGTV MSLAGKYTLN NWLATVTLGQ AGMHATYYHK ASDQLQVGVE FEASTRMQDT SVSFGYQLDL PKANLLFKGS VDS NWIVGA TLEKKLPPLP LTLALGAFLN HRKNKFQCGF GLTIG

UniProtKB: Mitochondrial import receptor subunit TOM40 homolog

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Macromolecule #3: Mitochondrial import receptor subunit TOM22 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM22 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.532528 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAAAVAAAGA GEPQSPDELL PKGDAEKPEE ELEEDDDEEL DETLSERLWG LTEMFPERVR SAAGATFDLS LFVAQKMYRF SRAALWIGT TSFMILVLPV VFETEKLQME QQQQLQQRQI LLGPNTGLSG GMPGALPSLP GKI

UniProtKB: Mitochondrial import receptor subunit TOM22 homolog

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Macromolecule #4: Mitochondrial import receptor subunit TOM5 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM5 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.045318 KDa
SequenceString:
MFRIEGLAPK LDPEEMKRKM REDVISSIRN FLIYVALLRV TPFILKKLDS I

UniProtKB: Mitochondrial import receptor subunit TOM5 homolog

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Macromolecule #5: Mitochondrial import receptor subunit TOM7 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM7 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.256473 KDa
SequenceString:
MVKLSKEAKQ RLQQLFKGSQ FAIRWGFIPL VIYLGFKRGA DPGMPEPTVL SLLWG

UniProtKB: Mitochondrial import receptor subunit TOM7 homolog

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Macromolecule #6: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.319862 KDa
SequenceString:
MVGRNSAIAA GVCGALFIGY CIYFDRKRRS DPNFKNRLRE RRKKQKLAKE RAGLSKLPDL KDAEAVQKFF LEEIQLGEEL LAQGEYEKG VDHLTNAIAV CGQPQQLLQV LQQTLPPPVF QMLLTKLPTI SQRIVSAQSL AEDDVE

UniProtKB: Mitochondrial import receptor subunit TOM20 homolog

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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: 7.4
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4SMOPS
150.0 mMKClpotassium chloride
0.1 %C56H92O29DIG
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 282 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1151405
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vdd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189667
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8xva:
Human TOM complex with whole Tom20

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