+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31888 | |||||||||
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Title | Tom complex with Tom22 and Tom20 subunits | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Tom complex / Cryo-EM / Tom22 / TRANSLOCASE | |||||||||
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: 3.74 Å | |||||||||
Authors | Liu DS / Sui SF | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Tom complex with Tom22 and Tom20 subunits Authors: Liu DS / Sui SF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31888.map.gz | 58.7 MB | EMDB map data format | |
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Header (meta data) | emd-31888-v30.xml emd-31888.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_31888.png | 112.5 KB | ||
Filedesc metadata | emd-31888.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31888 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31888 | HTTPS FTP |
-Validation report
Summary document | emd_31888_validation.pdf.gz | 451.8 KB | Display | EMDB validaton report |
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Full document | emd_31888_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | emd_31888_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_31888_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31888 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31888 | HTTPS FTP |
-Related structure data
Related structure data | 7vc4MC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31888.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Tom complex with full length Tom22 subunits
Entire | Name: Tom complex with full length Tom22 subunits |
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Components |
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-Supramolecule #1: Tom complex with full length Tom22 subunits
Supramolecule | Name: Tom complex with full length Tom22 subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Mitochondrial import receptor subunit TOM6 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM6 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: 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 #2: Mitochondrial import receptor subunit TOM40 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM40 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: 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 #3: Mitochondrial import receptor subunit TOM22 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM22 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: 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 #4: Mitochondrial import receptor subunit TOM5 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM5 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: 6.045318 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFRIEGLAPK LDPEEMKRKM REDVISSIRN FLIYVALLRV TPFILKKLDS I UniProtKB: Mitochondrial import receptor subunit TOM5 homolog |
-Macromolecule #5: Mitochondrial import receptor subunit TOM7 homolog
Macromolecule | Name: Mitochondrial import receptor subunit TOM7 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: 6.256473 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVKLSKEAKQ RLQQLFKGSQ FAIRWGFIPL VIYLGFKRGA DPGMPEPTVL SLLWG UniProtKB: Mitochondrial import receptor subunit TOM7 homolog |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: Digitinon |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347601 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |