+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30382 | |||||||||
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Title | Protein translocase of mitochondria | |||||||||
Map data | dimeric human TOM complex | |||||||||
Sample |
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Keywords | Complex / Mitochondria / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitophagy in response to mitochondrial depolarization / protein import into mitochondrial matrix / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane ...TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitophagy in response to mitochondrial depolarization / protein import into mitochondrial matrix / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Yang M / Wang W / Zhang L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2020 Title: Atomic structure of human TOM core complex. Authors: Wenhe Wang / Xudong Chen / Laixing Zhang / Jingbo Yi / Qingxi Ma / Jian Yin / Wei Zhuo / Jinke Gu / Maojun Yang / Abstract: The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle ...The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30382.map.gz | 9 MB | EMDB map data format | |
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Header (meta data) | emd-30382-v30.xml emd-30382.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_30382.png | 32.9 KB | ||
Filedesc metadata | emd-30382.cif.gz | 5.5 KB | ||
Others | emd_30382_additional_1.map.gz | 117.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30382 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30382 | HTTPS FTP |
-Validation report
Summary document | emd_30382_validation.pdf.gz | 396.6 KB | Display | EMDB validaton report |
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Full document | emd_30382_full_validation.pdf.gz | 396.2 KB | Display | |
Data in XML | emd_30382_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_30382_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30382 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30382 | HTTPS FTP |
-Related structure data
Related structure data | 7ck6MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30382.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | dimeric human TOM complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: tetrameric human TOM complex
File | emd_30382_additional_1.map | ||||||||||||
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Annotation | tetrameric human TOM complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The translocase of the outer mitochondrial membrane (TOM) complex
Entire | Name: The translocase of the outer mitochondrial membrane (TOM) complex |
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Components |
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-Supramolecule #1: The translocase of the outer mitochondrial membrane (TOM) complex
Supramolecule | Name: The translocase of the outer mitochondrial membrane (TOM) complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Mitochondrial import receptor subunit TOM40 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM40 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.926926 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Mitochondrial import receptor subunit TOM22 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM22 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.532528 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAAAVAAAGA GEPQSPDELL PKGDAEKPEE ELEEDDDEEL DETLSERLWG LTEMFPERVR SAAGATFDLS LFVAQKMYRF SRAALWIGT TSFMILVLPV VFETEKLQME QQQQLQQRQI LLGPNTGLSG GMPGALPSLP GKI UniProtKB: Mitochondrial import receptor subunit TOM22 homolog |
-Macromolecule #3: Mitochondrial import receptor subunit TOM6 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM6 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.007988 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASSTVPVSA AGSANETPEI PDNVGDWLRG VYRFATDRND FRRNLILNLG LFAAGVWLAR NLSDIDLMAP QPGV UniProtKB: Mitochondrial import receptor subunit TOM6 homolog |
-Macromolecule #4: Mitochondrial import receptor subunit TOM7 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM7 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 6.256473 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVKLSKEAKQ RLQQLFKGSQ FAIRWGFIPL VIYLGFKRGA DPGMPEPTVL SLLWG UniProtKB: Mitochondrial import receptor subunit TOM7 homolog |
-Macromolecule #5: Mitochondrial import receptor subunit TOM5 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM5 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 6.045318 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFRIEGLAPK LDPEEMKRKM REDVISSIRN FLIYVALLRV TPFILKKLDS I UniProtKB: Mitochondrial import receptor subunit TOM5 homolog |
-Macromolecule #6: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: PC1 |
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Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ChemComp-PC1: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159369 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: COMMON LINE |