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Yorodumi- EMDB-12919: Cryo-EM structure of late human 39S mitoribosome assembly interme... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12919 | |||||||||
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Title | Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1 | |||||||||
Map data | local resolution filtered map | |||||||||
Sample |
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Keywords | 39S mitoribosome / ribosome biogenesis / RIBOSOME | |||||||||
Function / homology | Function and homology information rRNA (guanosine-2'-O-)-methyltransferase activity / ribonucleoprotein granule / rRNA modification in the mitochondrion / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation ...rRNA (guanosine-2'-O-)-methyltransferase activity / ribonucleoprotein granule / rRNA modification in the mitochondrion / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / mitochondrial nucleoid / ribosomal large subunit binding / acyl binding / Complex I biogenesis / acyl carrier activity / Respiratory electron transport / RNA processing / mitochondrial respiratory chain complex I assembly / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / : / ribosomal large subunit biogenesis / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / fatty acid binding / mitochondrial membrane / aerobic respiration / fibrillar center / fatty acid biosynthetic process / chromosome / double-stranded RNA binding / ribosome biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / RNA helicase activity / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / RNA helicase / structural constituent of ribosome / mitochondrial matrix / hydrolase activity / translation / ribonucleoprotein complex / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / nucleolus / GTP binding / apoptotic process / magnesium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Cheng J / Berninghausen O | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: 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. | |||||||||
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_12919.map.gz | 105.2 MB | EMDB map data format | |
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Header (meta data) | emd-12919-v30.xml emd-12919.xml | 69.2 KB 69.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12919_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_12919.png | 135.5 KB | ||
Filedesc metadata | emd-12919.cif.gz | 15.2 KB | ||
Others | emd_12919_additional_1.map.gz emd_12919_additional_2.map.gz | 140.1 MB 139.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12919 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12919 | HTTPS FTP |
-Validation report
Summary document | emd_12919_validation.pdf.gz | 471.4 KB | Display | EMDB validaton report |
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Full document | emd_12919_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | emd_12919_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_12919_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12919 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12919 | HTTPS FTP |
-Related structure data
Related structure data | 7oi6MC 7oi7C 7oi8C 7oi9C 7oiaC 7oibC 7oicC 7oidC 7oieC 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_12919.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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: map without sharpening
File | emd_12919_additional_1.map | ||||||||||||
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Annotation | map without sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: map focus refined on MRM3-DDX28 region
File | emd_12919_additional_2.map | ||||||||||||
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Annotation | map focus refined on MRM3-DDX28 region | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human 39S mitoribosome assembly intermediates, state 1
+Supramolecule #1: Human 39S mitoribosome assembly intermediates, state 1
+Macromolecule #1: 39S ribosomal protein L2, mitochondrial
+Macromolecule #2: 39S ribosomal protein L3, mitochondrial
+Macromolecule #3: 39S ribosomal protein L4, mitochondrial
+Macromolecule #4: 39S ribosomal protein L9, mitochondrial
+Macromolecule #5: 39S ribosomal protein L13, mitochondrial
+Macromolecule #6: 39S ribosomal protein L14, mitochondrial
+Macromolecule #7: 39S ribosomal protein L15, mitochondrial
+Macromolecule #8: 39S ribosomal protein L16, mitochondrial
+Macromolecule #9: 39S ribosomal protein L17, mitochondrial
+Macromolecule #10: 39S ribosomal protein L19, mitochondrial
+Macromolecule #11: 39S ribosomal protein L20, mitochondrial
+Macromolecule #12: 39S ribosomal protein L21, mitochondrial
+Macromolecule #13: 39S ribosomal protein L22, mitochondrial
+Macromolecule #14: 39S ribosomal protein L23, mitochondrial
+Macromolecule #15: 39S ribosomal protein L24, mitochondrial
+Macromolecule #16: 39S ribosomal protein L28, mitochondrial
+Macromolecule #17: 39S ribosomal protein L47, mitochondrial
+Macromolecule #18: 39S ribosomal protein L30, mitochondrial
+Macromolecule #19: 39S ribosomal protein L32, mitochondrial
+Macromolecule #20: 39S ribosomal protein L34, mitochondrial
+Macromolecule #21: 39S ribosomal protein L37, mitochondrial
+Macromolecule #22: 39S ribosomal protein L39, mitochondrial
+Macromolecule #23: 39S ribosomal protein L41, mitochondrial
+Macromolecule #24: 39S ribosomal protein L42, mitochondrial
+Macromolecule #25: 39S ribosomal protein L43, mitochondrial
+Macromolecule #26: 39S ribosomal protein L44, mitochondrial
+Macromolecule #27: 39S ribosomal protein L45, mitochondrial
+Macromolecule #28: 39S ribosomal protein L49, mitochondrial
+Macromolecule #29: 39S ribosomal protein L50, mitochondrial
+Macromolecule #30: 39S ribosomal protein L51, mitochondrial
+Macromolecule #31: 39S ribosomal protein L52, mitochondrial
+Macromolecule #32: Ribosomal protein 63, mitochondrial
+Macromolecule #33: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #34: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #35: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #36: 39S ribosomal protein S30, mitochondrial
+Macromolecule #37: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #38: MIEF1 upstream open reading frame protein
+Macromolecule #39: Acyl carrier protein, mitochondrial
+Macromolecule #41: Probable ATP-dependent RNA helicase DDX28
+Macromolecule #42: GTP-binding protein 10
+Macromolecule #43: rRNA methyltransferase 3, mitochondrial
+Macromolecule #45: 39S ribosomal protein L18, mitochondrial
+Macromolecule #46: 39S ribosomal protein L27, mitochondrial
+Macromolecule #47: 39S ribosomal protein L38, mitochondrial
+Macromolecule #48: 39S ribosomal protein L10, mitochondrial
+Macromolecule #49: 39S ribosomal protein L11, mitochondrial
+Macromolecule #50: 39S ribosomal protein L53, mitochondrial
+Macromolecule #51: 39S ribosomal protein L54, mitochondrial
+Macromolecule #40: 16S rRNA
+Macromolecule #44: mitochondrial Val tRNA
+Macromolecule #52: MAGNESIUM ION
+Macromolecule #53: ZINC ION
+Macromolecule #54: 4'-PHOSPHOPANTETHEINE
-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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Vitrification | Cryogen name: ETHANE |
-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 |