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Yorodumi- EMDB-12925: Cryo-EM structure of late human 39S mitoribosome assembly interme... -
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Basic information
| Entry | Database: EMDB / ID: EMD-12925 | |||||||||
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| Title | Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4 | |||||||||
Map data | local resolution filtered map | |||||||||
Sample |
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Keywords | 39S mitoribosome / ribosome biogenesis / RIBOSOME | |||||||||
| Function / homology | Function and homology informationmRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / mitochondrial RNA modification / mitochondrial RNA catabolic process / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / Complex I biogenesis / protein lipoylation ...mRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / mitochondrial RNA modification / mitochondrial RNA catabolic process / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / Complex I biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / RNA methyltransferase activity / Respiratory electron transport / rRNA import into mitochondrion / rRNA methyltransferase activity / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / camera-type eye development / iron-sulfur cluster assembly complex / mitochondrial fission / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial large ribosomal subunit binding / mitochondrial ribosome / mitochondrial [2Fe-2S] assembly complex / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / rRNA methylation / mitochondrial translation / [2Fe-2S] cluster assembly / : / iron-sulfur cluster assembly / acyl binding / ribosomal large subunit binding / acyl carrier activity / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled cytosolic ribosome / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid binding / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / methyltransferase activity / mitochondrial membrane / fibrillar center / rRNA processing / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / heart development / 5S rRNA binding / double-stranded DNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / negative regulation of translation / mitochondrial inner membrane / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / regulation of DNA-templated transcription / nucleolus / structural molecule activity / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Cheng J / Berninghausen O | |||||||||
Citation | Journal: Nat Commun / Year: 2021Title: A distinct assembly pathway of the human 39S late pre-mitoribosome. Authors: Jingdong Cheng / Otto Berninghausen / Roland Beckmann / ![]() Abstract: Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. ...Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome. | |||||||||
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_12925.map.gz | 102.7 MB | EMDB map data format | |
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| Header (meta data) | emd-12925-v30.xml emd-12925.xml | 79.4 KB 79.4 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_12925_fsc.xml | 12.8 KB | Display | FSC data file |
| Images | emd_12925.png | 156.8 KB | ||
| Filedesc metadata | emd-12925.cif.gz | 16.9 KB | ||
| Others | emd_12925_additional_1.map.gz | 139.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12925 | HTTPS FTP |
-Validation report
| Summary document | emd_12925_validation.pdf.gz | 484.6 KB | Display | EMDB validaton report |
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| Full document | emd_12925_full_validation.pdf.gz | 484.2 KB | Display | |
| Data in XML | emd_12925_validation.xml.gz | 13.3 KB | Display | |
| Data in CIF | emd_12925_validation.cif.gz | 18 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12925 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12925 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7oicMC ![]() 7oi6C ![]() 7oi7C ![]() 7oi8C ![]() 7oi9C ![]() 7oiaC ![]() 7oibC ![]() 7oidC ![]() 7oieC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_12925.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Annotation | local resolution filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unfiltered map
| File | emd_12925_additional_1.map | ||||||||||||
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| Annotation | Unfiltered map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Human 39S mitoribosome assembly intermediates, state 4
+Supramolecule #1: Human 39S mitoribosome assembly intermediates, state 4
+Macromolecule #1: 16S rRNA
+Macromolecule #2: mitochondrial Val tRNA
+Macromolecule #58: RNA pCpA
+Macromolecule #3: Large ribosomal subunit protein uL2m
+Macromolecule #4: Large ribosomal subunit protein uL3m
+Macromolecule #5: Large ribosomal subunit protein uL4m
+Macromolecule #6: Large ribosomal subunit protein bL9m
+Macromolecule #7: Large ribosomal subunit protein uL10m
+Macromolecule #8: Large ribosomal subunit protein uL11m
+Macromolecule #9: Large ribosomal subunit protein uL13m
+Macromolecule #10: Large ribosomal subunit protein uL14m
+Macromolecule #11: Large ribosomal subunit protein uL15m
+Macromolecule #12: Large ribosomal subunit protein uL16m
+Macromolecule #13: Large ribosomal subunit protein bL17m
+Macromolecule #14: Large ribosomal subunit protein uL18m
+Macromolecule #15: Large ribosomal subunit protein bL19m
+Macromolecule #16: Large ribosomal subunit protein bL20m
+Macromolecule #17: Large ribosomal subunit protein bL21m
+Macromolecule #18: Large ribosomal subunit protein uL22m
+Macromolecule #19: Large ribosomal subunit protein uL23m
+Macromolecule #20: Large ribosomal subunit protein uL24m
+Macromolecule #21: Large ribosomal subunit protein bL27m
+Macromolecule #22: Large ribosomal subunit protein bL28m
+Macromolecule #23: Large ribosomal subunit protein uL29m
+Macromolecule #24: Large ribosomal subunit protein uL30m
+Macromolecule #25: Large ribosomal subunit protein bL32m
+Macromolecule #26: Large ribosomal subunit protein bL33m
+Macromolecule #27: Large ribosomal subunit protein bL34m
+Macromolecule #28: Large ribosomal subunit protein bL35m
+Macromolecule #29: Large ribosomal subunit protein bL36m
+Macromolecule #30: Large ribosomal subunit protein mL37
+Macromolecule #31: Large ribosomal subunit protein mL38
+Macromolecule #32: Large ribosomal subunit protein mL39
+Macromolecule #33: Large ribosomal subunit protein mL40
+Macromolecule #34: Large ribosomal subunit protein mL41
+Macromolecule #35: Large ribosomal subunit protein mL42
+Macromolecule #36: Large ribosomal subunit protein mL43
+Macromolecule #37: Large ribosomal subunit protein mL44
+Macromolecule #38: 39S ribosomal protein L45, mitochondrial
+Macromolecule #39: Large ribosomal subunit protein mL46
+Macromolecule #40: Large ribosomal subunit protein mL48
+Macromolecule #41: Large ribosomal subunit protein mL49
+Macromolecule #42: Large ribosomal subunit protein mL50
+Macromolecule #43: Large ribosomal subunit protein mL51
+Macromolecule #44: Large ribosomal subunit protein mL52
+Macromolecule #45: Large ribosomal subunit protein mL53
+Macromolecule #46: Large ribosomal subunit protein mL54
+Macromolecule #47: Large ribosomal subunit protein mL55
+Macromolecule #48: Large ribosomal subunit protein mL63
+Macromolecule #49: Large ribosomal subunit protein mL62
+Macromolecule #50: Large ribosomal subunit protein mL64
+Macromolecule #51: Large ribosomal subunit protein mL66
+Macromolecule #52: Large ribosomal subunit protein mL65
+Macromolecule #53: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #54: MIEF1 upstream open reading frame protein
+Macromolecule #55: Acyl carrier protein, mitochondrial
+Macromolecule #56: 5-cytosine rRNA methyltransferase NSUN4
+Macromolecule #57: Transcription termination factor 4, mitochondrial
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: ZINC ION
+Macromolecule #61: 4'-PHOSPHOPANTETHEINE
+Macromolecule #62: S-ADENOSYLMETHIONINE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 28.0 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 |
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Keywords
Homo sapiens (human)
Authors
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