[English] 日本語
Yorodumi- EMDB-12847: State C of the human mitoribosomal large subunit assembly intermediate -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12847 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | State C of the human mitoribosomal large subunit assembly intermediate | ||||||||||||
Map data | state C | ||||||||||||
Sample |
| ||||||||||||
Keywords | mitoribosome / assembly intermediate / large subunit / LSU / mt-LSU / RIBOSOME | ||||||||||||
Function / homology | Function and homology information regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation ...regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / rRNA methyltransferase activity / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial translational termination / mitochondrial transcription / mitochondrial large ribosomal subunit binding / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / protein targeting to mitochondrion / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / camera-type eye development / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / rRNA methylation / acyl binding / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / iron-sulfur cluster assembly / acyl carrier activity / mitochondrial translation / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ribosomal large subunit binding / anatomical structure morphogenesis / RNA processing / rescue of stalled ribosome / aerobic respiration / ribosomal large subunit biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / small ribosomal subunit rRNA binding / fibrillar center / rRNA processing / fatty acid biosynthetic process / large ribosomal subunit rRNA binding / double-stranded RNA binding / ribosome biogenesis / cell junction / heart development / 5S rRNA binding / double-stranded DNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / GTPase activity / synapse / apoptotic process / calcium ion binding / GTP binding / nucleolus / regulation of DNA-templated transcription / magnesium ion binding / 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 | Lenarcic T / Jaskolowski M / Leibundgut M / Scaiola A / Schoenhut T / Saurer M / Lee RG / Rackham O / Filipovska A / Ban N | ||||||||||||
Funding support | Switzerland, 3 items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Stepwise maturation of the peptidyl transferase region of human mitoribosomes. Authors: Tea Lenarčič / Mateusz Jaskolowski / Marc Leibundgut / Alain Scaiola / Tanja Schönhut / Martin Saurer / Richard G Lee / Oliver Rackham / Aleksandra Filipovska / Nenad Ban / Abstract: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral ...Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12847.map.gz | 324.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12847-v30.xml emd-12847.xml | 76.3 KB 76.3 KB | Display Display | EMDB header |
Images | emd_12847.png | 109 KB | ||
Filedesc metadata | emd-12847.cif.gz | 16.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12847 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12847 | HTTPS FTP |
-Related structure data
Related structure data | 7odtMC 7odrC 7odsC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_12847.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | state C | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : State C of the human mitoribosomal large subunit assembly intermediate
+Supramolecule #1: State C of the human mitoribosomal large subunit assembly intermediate
+Macromolecule #1: Mitochondrial ribosome-associated GTPase 2
+Macromolecule #2: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #3: MIEF1 upstream open reading frame protein
+Macromolecule #4: Acyl carrier protein, mitochondrial
+Macromolecule #5: 5-methylcytosine rRNA methyltransferase NSUN4
+Macromolecule #6: Transcription termination factor 4, mitochondrial
+Macromolecule #7: 39S ribosomal protein L32, mitochondrial
+Macromolecule #8: 39S ribosomal protein L33, mitochondrial
+Macromolecule #9: 39S ribosomal protein L34, mitochondrial
+Macromolecule #10: 39S ribosomal protein L35, mitochondrial
+Macromolecule #11: 39S ribosomal protein L36, mitochondrial
+Macromolecule #12: 39S ribosomal protein L37, mitochondrial
+Macromolecule #13: 39S ribosomal protein L38, mitochondrial
+Macromolecule #14: 39S ribosomal protein L39, mitochondrial
+Macromolecule #15: 39S ribosomal protein L40, mitochondrial
+Macromolecule #16: 39S ribosomal protein L41, mitochondrial
+Macromolecule #19: 39S ribosomal protein L2, mitochondrial
+Macromolecule #20: 39S ribosomal protein L3, mitochondrial
+Macromolecule #21: 39S ribosomal protein L4, mitochondrial
+Macromolecule #22: 39S ribosomal protein L9, mitochondrial
+Macromolecule #23: 39S ribosomal protein L10, mitochondrial
+Macromolecule #24: 39S ribosomal protein L11, mitochondrial
+Macromolecule #25: 39S ribosomal protein L13, mitochondrial
+Macromolecule #26: 39S ribosomal protein L14, mitochondrial
+Macromolecule #27: 39S ribosomal protein L15, mitochondrial
+Macromolecule #28: 39S ribosomal protein L16, mitochondrial
+Macromolecule #29: 39S ribosomal protein L17, mitochondrial
+Macromolecule #30: 39S ribosomal protein L18, mitochondrial
+Macromolecule #31: 39S ribosomal protein L19, mitochondrial
+Macromolecule #32: 39S ribosomal protein L20, mitochondrial
+Macromolecule #33: 39S ribosomal protein L21, mitochondrial
+Macromolecule #34: 39S ribosomal protein L22, mitochondrial
+Macromolecule #35: 39S ribosomal protein L23, mitochondrial
+Macromolecule #36: 39S ribosomal protein L24, mitochondrial
+Macromolecule #37: 39S ribosomal protein L27, mitochondrial
+Macromolecule #38: 39S ribosomal protein L28, mitochondrial
+Macromolecule #39: 39S ribosomal protein L47, mitochondrial
+Macromolecule #40: 39S ribosomal protein L30, mitochondrial
+Macromolecule #41: 39S ribosomal protein L42, mitochondrial
+Macromolecule #42: 39S ribosomal protein L43, mitochondrial
+Macromolecule #43: 39S ribosomal protein L44, mitochondrial
+Macromolecule #44: 39S ribosomal protein L45, mitochondrial
+Macromolecule #45: 39S ribosomal protein L46, mitochondrial
+Macromolecule #46: 39S ribosomal protein L48, mitochondrial
+Macromolecule #47: 39S ribosomal protein L49, mitochondrial
+Macromolecule #48: 39S ribosomal protein L50, mitochondrial
+Macromolecule #49: 39S ribosomal protein L51, mitochondrial
+Macromolecule #50: 39S ribosomal protein L52, mitochondrial
+Macromolecule #51: 39S ribosomal protein L53, mitochondrial
+Macromolecule #52: 39S ribosomal protein L54, mitochondrial
+Macromolecule #53: 39S ribosomal protein L55, mitochondrial
+Macromolecule #54: Ribosomal protein 63, mitochondrial
+Macromolecule #55: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #56: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #57: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #58: 39S ribosomal protein S30, mitochondrial
+Macromolecule #17: 16S mitochondrial rRNA
+Macromolecule #18: mitochondrial tRNAVal
+Macromolecule #59: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYL...
+Macromolecule #62: S-ADENOSYLMETHIONINE
+Macromolecule #63: ZINC ION
+Macromolecule #64: POTASSIUM ION
+Macromolecule #65: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS | ||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 4 uL of the sample was blotted for 2-6 sec before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 62552 |