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Yorodumi- EMDB-11642: Structure of the elongating human mitoribosome bound to mtEF-Tu.G... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11642 | ||||||||||||
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Title | Structure of the elongating human mitoribosome bound to mtEF-Tu.GMPPCP and A/T mt-tRNA | ||||||||||||
Map data | Human mitoribosome bound to mtEF-Tu.GMPPCP and A/T tRNA | ||||||||||||
Sample |
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Keywords | mitochondrial ribosome / ribosome stalling / cryo-EM / RIBOSOME | ||||||||||||
Function / homology | Function and homology information SARS-CoV-2 modulates autophagy / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination ...SARS-CoV-2 modulates autophagy / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / mitochondrial large ribosomal subunit / negative regulation of mitotic nuclear division / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / mitochondrial nucleoid / positive regulation of proteolysis / translational elongation / ribosomal small subunit binding / anatomical structure morphogenesis / translation elongation factor activity / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / double-stranded RNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit / cell junction / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / nuclear membrane / endonuclease activity / response to ethanol / mitochondrial outer membrane / cell population proliferation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / nucleotide binding / synapse / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.33 Å | ||||||||||||
Authors | Desai N / Yang H | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Science / Year: 2020 Title: Elongational stalling activates mitoribosome-associated quality control. Authors: Nirupa Desai / Hanting Yang / Viswanathan Chandrasekaran / Razina Kazi / Michal Minczuk / V Ramakrishnan / Abstract: The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a ...The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase. | ||||||||||||
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_11642.map.gz | 57.6 MB | EMDB map data format | |
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Header (meta data) | emd-11642-v30.xml emd-11642.xml | 128.7 KB 128.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11642_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_11642.png | 210.5 KB | ||
Filedesc metadata | emd-11642.cif.gz | 22.9 KB | ||
Others | emd_11642_additional_1.map.gz emd_11642_half_map_1.map.gz emd_11642_half_map_2.map.gz | 410.8 MB 411.4 MB 411.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11642 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11642 | HTTPS FTP |
-Validation report
Summary document | emd_11642_validation.pdf.gz | 922.5 KB | Display | EMDB validaton report |
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Full document | emd_11642_full_validation.pdf.gz | 922.1 KB | Display | |
Data in XML | emd_11642_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | emd_11642_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11642 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11642 | HTTPS FTP |
-Related structure data
Related structure data | 7a5gMC 7a5fC 7a5hC 7a5iC 7a5jC 7a5kC 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_11642.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human mitoribosome bound to mtEF-Tu.GMPPCP and A/T tRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unprocessed map
File | emd_11642_additional_1.map | ||||||||||||
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Annotation | Unprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map
File | emd_11642_half_map_1.map | ||||||||||||
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Annotation | Half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 map
File | emd_11642_half_map_2.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human mitoribosome
+Supramolecule #1: human mitoribosome
+Supramolecule #2: human mitoribosome
+Supramolecule #3: 50S ribosomal protein L1 homology model
+Macromolecule #1: nascent chain
+Macromolecule #4: 39S ribosomal protein L2, mitochondrial
+Macromolecule #5: 39S ribosomal protein L3, mitochondrial
+Macromolecule #6: 39S ribosomal protein L4, mitochondrial
+Macromolecule #7: 39S ribosomal protein L9, mitochondrial
+Macromolecule #8: 39S ribosomal protein L10, mitochondrial
+Macromolecule #9: 39S ribosomal protein L11, mitochondrial
+Macromolecule #10: 39S ribosomal protein L13, mitochondrial
+Macromolecule #11: 39S ribosomal protein L14, mitochondrial
+Macromolecule #12: 39S ribosomal protein L15, mitochondrial
+Macromolecule #13: 39S ribosomal protein L16, mitochondrial
+Macromolecule #14: 39S ribosomal protein L17, mitochondrial
+Macromolecule #15: 39S ribosomal protein L18, mitochondrial
+Macromolecule #16: 39S ribosomal protein L19, mitochondrial
+Macromolecule #17: 39S ribosomal protein L20, mitochondrial
+Macromolecule #18: 39S ribosomal protein L21, mitochondrial
+Macromolecule #19: 39S ribosomal protein L22, mitochondrial
+Macromolecule #20: 39S ribosomal protein L23, mitochondrial
+Macromolecule #21: 39S ribosomal protein L24, mitochondrial
+Macromolecule #22: 39S ribosomal protein L27, mitochondrial
+Macromolecule #23: 39S ribosomal protein L28, mitochondrial
+Macromolecule #24: 39S ribosomal protein L47, mitochondrial
+Macromolecule #25: 39S ribosomal protein L30, mitochondrial
+Macromolecule #26: 39S ribosomal protein L32, mitochondrial
+Macromolecule #27: 39S ribosomal protein L33, mitochondrial
+Macromolecule #28: 39S ribosomal protein L34, mitochondrial
+Macromolecule #29: 39S ribosomal protein L35, mitochondrial
+Macromolecule #30: 39S ribosomal protein L36, mitochondrial
+Macromolecule #31: 39S ribosomal protein L37, mitochondrial
+Macromolecule #32: 39S ribosomal protein L38, mitochondrial
+Macromolecule #33: 39S ribosomal protein L39, mitochondrial
+Macromolecule #34: 39S ribosomal protein L41, mitochondrial
+Macromolecule #35: 39S ribosomal protein L42, mitochondrial
+Macromolecule #36: 39S ribosomal protein L43, mitochondrial
+Macromolecule #37: 39S ribosomal protein L44, mitochondrial
+Macromolecule #38: 39S ribosomal protein L45, mitochondrial
+Macromolecule #39: 39S ribosomal protein L46, mitochondrial
+Macromolecule #40: 39S ribosomal protein L48, mitochondrial
+Macromolecule #41: 39S ribosomal protein L49, mitochondrial
+Macromolecule #42: 39S ribosomal protein L50, mitochondrial
+Macromolecule #43: 39S ribosomal protein L51, mitochondrial
+Macromolecule #44: 39S ribosomal protein L52, mitochondrial
+Macromolecule #45: 39S ribosomal protein L53, mitochondrial
+Macromolecule #46: 39S ribosomal protein L54, mitochondrial
+Macromolecule #47: 39S ribosomal protein L55, mitochondrial
+Macromolecule #48: Ribosomal protein 63, mitochondrial
+Macromolecule #49: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #50: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #51: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #52: 39S ribosomal protein S30, mitochondrial,39S ribosomal protein S3...
+Macromolecule #54: Oxa1L tail
+Macromolecule #55: 28S ribosomal protein S2, mitochondrial
+Macromolecule #56: 28S ribosomal protein S24, mitochondrial
+Macromolecule #57: 28S ribosomal protein S5, mitochondrial
+Macromolecule #58: 28S ribosomal protein S6, mitochondrial
+Macromolecule #59: 28S ribosomal protein S7, mitochondrial
+Macromolecule #60: 28S ribosomal protein S9, mitochondrial
+Macromolecule #61: 28S ribosomal protein S10, mitochondrial
+Macromolecule #62: 28S ribosomal protein S11, mitochondrial
+Macromolecule #63: 28S ribosomal protein S12, mitochondrial
+Macromolecule #64: 28S ribosomal protein S14, mitochondrial
+Macromolecule #65: 28S ribosomal protein S15, mitochondrial
+Macromolecule #66: 28S ribosomal protein S16, mitochondrial
+Macromolecule #67: 28S ribosomal protein S17, mitochondrial
+Macromolecule #68: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #69: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #70: 28S ribosomal protein S21, mitochondrial
+Macromolecule #71: 28S ribosomal protein S22, mitochondrial
+Macromolecule #72: 28S ribosomal protein S23, mitochondrial
+Macromolecule #73: 28S ribosomal protein S25, mitochondrial
+Macromolecule #74: 28S ribosomal protein S26, mitochondrial
+Macromolecule #75: 28S ribosomal protein S27, mitochondrial
+Macromolecule #76: 28S ribosomal protein S28, mitochondrial
+Macromolecule #77: 28S ribosomal protein S29, mitochondrial
+Macromolecule #78: 28S ribosomal protein S31, mitochondrial
+Macromolecule #79: 28S ribosomal protein S33, mitochondrial
+Macromolecule #80: 28S ribosomal protein S34, mitochondrial
+Macromolecule #81: 28S ribosomal protein S35, mitochondrial
+Macromolecule #82: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #83: Aurora kinase A-interacting protein
+Macromolecule #84: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #88: 39S ribosomal protein L40, mitochondrial
+Macromolecule #89: Elongation factor Tu, mitochondrial
+Macromolecule #91: 50S ribosomal protein L1
+Macromolecule #2: 16S rRNA
+Macromolecule #3: mt-tRNAVal
+Macromolecule #53: RNA (5'-R(P*CP*A)-3')
+Macromolecule #85: 12S rRNA
+Macromolecule #86: P tRNA
+Macromolecule #87: mRNA
+Macromolecule #90: E tRNA
+Macromolecule #92: MAGNESIUM ION
+Macromolecule #93: SPERMIDINE
+Macromolecule #94: ZINC ION
+Macromolecule #95: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #96: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #97: SODIUM ION
+Macromolecule #98: SULFATE ION
+Macromolecule #99: MALONATE ION
+Macromolecule #100: CHLORIDE ION
+Macromolecule #101: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / 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 |