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Yorodumi- EMDB-9958: Cryo-EM structure of the human mitochondrial translocase TIM22 co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9958 | |||||||||
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Title | Cryo-EM structure of the human mitochondrial translocase TIM22 complex at 3.7 angstrom. | |||||||||
Map data | The overall cryo-EM map of TIM22 complex at 3.7 angstrom. | |||||||||
Sample |
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Function / homology | Function and homology information ceramide kinase / acylglycerol kinase / ceramide kinase activity / acylglycerol kinase activity / dihydroceramide kinase activity / Glycerophospholipid biosynthesis / mitochondrial intermembrane space protein transporter complex / glycerolipid metabolic process / : / lipid kinase activity ...ceramide kinase / acylglycerol kinase / ceramide kinase activity / acylglycerol kinase activity / dihydroceramide kinase activity / Glycerophospholipid biosynthesis / mitochondrial intermembrane space protein transporter complex / glycerolipid metabolic process / : / lipid kinase activity / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / membrane insertase activity / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / TIM22 mitochondrial import inner membrane insertion complex / NAD+ kinase activity / protein transporter activity / protein insertion into mitochondrial inner membrane / sphingolipid metabolic process / ceramide biosynthetic process / Mitochondrial protein import / protein targeting to mitochondrion / protein transmembrane transporter activity / Mitochondrial protein degradation / cell-matrix adhesion / mitochondrial membrane / sensory perception of sound / mitochondrial intermembrane space / Signaling by BRAF and RAF1 fusions / protein-folding chaperone binding / mitochondrial outer membrane / mitochondrial inner membrane / membrane => GO:0016020 / phosphorylation / intracellular membrane-bounded organelle / protein homodimerization activity / mitochondrion / zinc ion binding / ATP binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Qi L / Wang Q / Guan Z / Yan C / Yin P | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Res / Year: 2021 Title: Cryo-EM structure of the human mitochondrial translocase TIM22 complex. Authors: Liangbo Qi / Qiang Wang / Zeyuan Guan / Yan Wu / Cuicui Shen / Sixing Hong / Jianbo Cao / Xing Zhang / Chuangye Yan / Ping Yin / | |||||||||
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_9958.map.gz | 116.5 MB | EMDB map data format | |
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Header (meta data) | emd-9958-v30.xml emd-9958.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
Images | emd_9958.png | 135.6 KB | ||
Others | emd_9958_additional_1.map.gz | 115.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9958 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9958 | HTTPS FTP |
-Validation report
Summary document | emd_9958_validation.pdf.gz | 453.4 KB | Display | EMDB validaton report |
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Full document | emd_9958_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | emd_9958_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_9958_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9958 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9958 | HTTPS FTP |
-Related structure data
Related structure data | 7cgpMC 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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-Map
File | Download / File: emd_9958.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The overall cryo-EM map of TIM22 complex at 3.7 angstrom. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: The cryo-EM map for inter-membrane region of TIM22...
File | emd_9958_additional_1.map | ||||||||||||
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Annotation | The cryo-EM map for inter-membrane region of TIM22 complex at 3.5 angstrom. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TIM22 translocase
Entire | Name: TIM22 translocase |
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Components |
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-Supramolecule #1: TIM22 translocase
Supramolecule | Name: TIM22 translocase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
Molecular weight | Theoretical: 220 kDa/nm |
-Macromolecule #1: Mitochondrial import inner membrane translocase subunit Tim22
Macromolecule | Name: Mitochondrial import inner membrane translocase subunit Tim22 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20.04893 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAAAAPNAGG SAPETAGSAE APLQYSLLLQ YLVGDKRQPR LLEPGSLGGI PSPAKSEEQK MIEKAMESCA FKAALACVGG FVLGGAFGV FTAGIDTNVG FDPKDPYRTP TAKEVLKDMG QRGMSYAKNF AIVGAMFSCT ECLIESYRGT SDWKNSVISG C ITGGAIGF ...String: MAAAAPNAGG SAPETAGSAE APLQYSLLLQ YLVGDKRQPR LLEPGSLGGI PSPAKSEEQK MIEKAMESCA FKAALACVGG FVLGGAFGV FTAGIDTNVG FDPKDPYRTP TAKEVLKDMG QRGMSYAKNF AIVGAMFSCT ECLIESYRGT SDWKNSVISG C ITGGAIGF RAGLKAGAIG CGGFAAFSAA IDYYLR |
-Macromolecule #2: Acylglycerol kinase, mitochondrial
Macromolecule | Name: Acylglycerol kinase, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: diacylglycerol kinase (ATP) |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.196008 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTVFFKTLRN HWKKTTAGLC LLTWGGHWLY GKHCDNLLRR AACQEAQVFG NQLIPPNAQV KKATVFLNPA ACKGKARTLF EKNAAPILH LSGMDVTIVK TDYEGQAKKL LELMENTDVI IVAGGDGTLQ EVVTGVLRRT DEATFSKIPI GFIPLGETSS L SHTLFAES ...String: MTVFFKTLRN HWKKTTAGLC LLTWGGHWLY GKHCDNLLRR AACQEAQVFG NQLIPPNAQV KKATVFLNPA ACKGKARTLF EKNAAPILH LSGMDVTIVK TDYEGQAKKL LELMENTDVI IVAGGDGTLQ EVVTGVLRRT DEATFSKIPI GFIPLGETSS L SHTLFAES GNKVQHITDA TLAIVKGETV PLDVLQIKGE KEQPVFAMTG LRWGSFRDAG VKVSKYWYLG PLKIKAAHFF ST LKEWPQT HQASISYTGP TERPPNEPEE TPVQRPSLYR RILRRLASYW AQPQDALSQE VSPEVWKDVQ LSTIELSITT RNN QLDPTS KEDFLNICIE PDTISKGDFI TIGSRKVRNP KLHVEGTECL QASQCTLLIP EGAGGSFSID SEEYEAMPVE VKLL PRKLQ FFCDPRKREQ MLTSPTQ |
-Macromolecule #3: Mitochondrial import inner membrane translocase subunit Tim29
Macromolecule | Name: Mitochondrial import inner membrane translocase subunit Tim29 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.272336 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAAAALRRFW SRRRAEAGDA VVAKPGVWAR LGSWARALLR DYAEACRDAS AEARARPGRA AVYVGLLGGA AACFTLAPSE GAFEEALLE ASGTLLLLAP ATRNRESEAF VQRLLWLRGR GRLRYVNLGL CSLVYEAPFD AQASLYQARC RYLQPRWTDF P GRVLDVGF ...String: MAAAALRRFW SRRRAEAGDA VVAKPGVWAR LGSWARALLR DYAEACRDAS AEARARPGRA AVYVGLLGGA AACFTLAPSE GAFEEALLE ASGTLLLLAP ATRNRESEAF VQRLLWLRGR GRLRYVNLGL CSLVYEAPFD AQASLYQARC RYLQPRWTDF P GRVLDVGF VGRWWVLGAW MRDCDINDDE FLHLPAHLRV VGPQQLHSET NERLFDEKYK PVVLTDDQVD QALWEEQVLQ KE KKDRLAL SQAHSLVQAE APR |
-Macromolecule #4: Mitochondrial import inner membrane translocase subunit Tim9
Macromolecule | Name: Mitochondrial import inner membrane translocase subunit Tim9 type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.391906 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAAQIPESDQ IKQFKEFLGT YNKLTETCFL DCVKDFTTRE VKPEETTCSE HCLQKYLKMT QRISMRFQEY HIQQNEALAA KAGLLGQPR |
-Macromolecule #5: Mitochondrial import inner membrane translocase subunit Tim10
Macromolecule | Name: Mitochondrial import inner membrane translocase subunit Tim10 type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.348999 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDPLRAQQLA AELEVEMMAD MYNRMTSACH RKCVPPHYKE AELSKGESVC LDRCVSKYLD IHERMGKKLT ELSMQDEELM KRVQQSSGP A |
-Macromolecule #6: Mitochondrial import inner membrane translocase subunit Tim10 B
Macromolecule | Name: Mitochondrial import inner membrane translocase subunit Tim10 B type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.601244 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MERQQQQQQQ LRNLRDFLLV YNRMTELCFQ RCVPSLHHRA LDAEEEACLH SCAGKLIHSN HRLMAAYVQL MPALVQRRIA DYEAASAVP GVAAEQPGVS PSGS |
-Macromolecule #7: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
Macromolecule | Name: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 7 / Number of copies: 1 / Formula: PEE |
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Molecular weight | Theoretical: 749.073 Da |
Chemical component information | ChemComp-PEE: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7 mg/mL |
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Buffer | pH: 6 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |