+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34660 | |||||||||
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Title | Substrate-engaged TOM complex from yeast | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mitochondrial protein import / TOM / protein translocation / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / 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 translocase complex assembly / mitochondrial outer membrane translocase complex / 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 | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Aequorea victoria (jellyfish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Zhou XY / Yang YQ / Wang GP / Wang SS | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex. Authors: Xueyin Zhou / Yuqi Yang / Guopeng Wang / Shanshan Wang / Dongjie Sun / Xiaomin Ou / Yuke Lian / Long Li / Abstract: Over half of mitochondrial proteins are imported from the cytosol via the pre-sequence pathway, controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. The ...Over half of mitochondrial proteins are imported from the cytosol via the pre-sequence pathway, controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. The mechanisms through which proteins are translocated via the TOM and TIM23 complexes remain unclear. Here we report the assembly of the active TOM-TIM23 supercomplex of Saccharomyces cerevisiae with translocating polypeptide substrates. Electron cryo-microscopy analyses reveal that the polypeptide substrates pass the TOM complex through the center of a Tom40 subunit, interacting with a glutamine-rich region. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17 and Mgr2. The polypeptide substrates are shielded from lipids by Mgr2 and Tim17, which creates a translocation pathway characterized by a negatively charged entrance and a central hydrophobic region. These findings reveal an unexpected pre-sequence pathway through the TOM-TIM23 supercomplex spanning the double membranes of mitochondria. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34660.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-34660-v30.xml emd-34660.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34660_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_34660.png | 24.8 KB | ||
Filedesc metadata | emd-34660.cif.gz | 6.5 KB | ||
Others | emd_34660_half_map_1.map.gz emd_34660_half_map_2.map.gz | 65.4 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34660 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34660 | HTTPS FTP |
-Validation report
Summary document | emd_34660_validation.pdf.gz | 778.4 KB | Display | EMDB validaton report |
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Full document | emd_34660_full_validation.pdf.gz | 778 KB | Display | |
Data in XML | emd_34660_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_34660_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34660 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34660 | HTTPS FTP |
-Related structure data
Related structure data | 8hcoMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34660.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34660_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34660_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Substrate-engaged TOM complex from yeast
Entire | Name: Substrate-engaged TOM complex from yeast |
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Components |
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-Supramolecule #1: Substrate-engaged TOM complex from yeast
Supramolecule | Name: Substrate-engaged TOM complex from yeast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
-Macromolecule #1: Mitochondrial import receptor subunit TOM40
Macromolecule | Name: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 42.071141 KDa |
Sequence | String: 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 L UniProtKB: Mitochondrial import receptor subunit TOM40 |
-Macromolecule #2: Mitochondrial import receptor subunit TOM22
Macromolecule | Name: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 16.801373 KDa |
Sequence | String: MVELTEIKDD VVQLDEPQFS RNQAIVEEKA SATNNDVVDD EDDSDSDFED EFDENETLLD RIVALKDIVP PGKRQTISNF FGFTSSFVR NAFTKSGNLA WTLTTTALLL GVPLSLSILA EQQLIEMEKT FDLQSDANNI LAQGEKDAAA TAN UniProtKB: Mitochondrial import receptor subunit TOM22 |
-Macromolecule #3: Mitochondrial import receptor subunit TOM5
Macromolecule | Name: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 5.993924 KDa |
Sequence | String: MFGLPQQEVS EEEKRAHQEQ TEKTLKQAAY VAAFLWVSPM IWHLVKKQWK UniProtKB: Mitochondrial import receptor subunit TOM5 |
-Macromolecule #4: Mitochondrial import receptor subunit TOM6
Macromolecule | Name: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 6.41046 KDa |
Sequence | String: MDGMFAMPGA AAGAASPQQP KSRFQAFKES PLYTIALNGA FFVAGVAFIQ SPLMDMLAPQ L UniProtKB: Mitochondrial import receptor subunit TOM6 |
-Macromolecule #5: Mitochondrial import receptor subunit TOM7
Macromolecule | Name: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 6.876955 KDa |
Sequence | String: MSFLPSFILS DESKERISKI LTLTHNVAHY GWIPFVLYLG WAHTSNRPNF LNLLSPLPSV UniProtKB: Mitochondrial import receptor subunit TOM7 |
-Macromolecule #6: sfGFP
Macromolecule | Name: sfGFP / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aequorea victoria (jellyfish) |
Molecular weight | Theoretical: 61.514633 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: YGSTVPKSKS FEQDSSSVAY LNWHNGQIDN EPKLDMNKQK ISPAEVAKHN KPDDCWVVIN GYVYDLTRFL PNHPGMISLI AALAVDRVI GMENAMPWNL PADLAWFKRN TLNKPVIMGR HTWESIGRPL PGRKNIILSS QPGTDDRVTW VKSVDEAIAA S GDVPEIMV ...String: YGSTVPKSKS FEQDSSSVAY LNWHNGQIDN EPKLDMNKQK ISPAEVAKHN KPDDCWVVIN GYVYDLTRFL PNHPGMISLI AALAVDRVI GMENAMPWNL PADLAWFKRN TLNKPVIMGR HTWESIGRPL PGRKNIILSS QPGTDDRVTW VKSVDEAIAA S GDVPEIMV IGGGRVYEQF LPKAQKLYLT HIDAEVEGDT HFPDYEPDDW ESVFSEFHDA DAQNSHSYSF EILERRGQDV IK FNAGKDV TAIFEPLHAP NVIDKYIAPE KKLGPLQGSG SGSKGEELFT GVVPILVELD GDVNGHKFSV RGEGEGDATN GKL TLKFIC TTGKLPVPWP TLVTTF(GYS)VQC FSRYPDHMKR HDFFKSAMPE GYVQERTISF KDDGTYKTRA EVKFEGDTLV NRIELKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN GIKANFKIRH NVEDGSVQLA DHYQQNTPIG DGPVLLPDNH Y LSTQSVLS KDPNEKRDHM VLLEFVTAAG ITHGSAGLEV LFQGPANGGS AWSHPQFEKG GGSGGGSGGG SWSHPQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |