+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31465 | |||||||||
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Title | human delta-METTL18 60S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / embryonic brain development / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / GAIT complex / middle ear morphogenesis ...eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / embryonic brain development / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / GAIT complex / middle ear morphogenesis / A band / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / optic nerve development / response to aldosterone / retinal ganglion cell axon guidance / homeostatic process / G1 to G0 transition / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / protein-RNA complex assembly / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / maturation of LSU-rRNA / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / cytosolic ribosome / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / embryo implantation / VLDLR internalisation and degradation / bone development / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / ossification / Regulation of BACH1 activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Takahashi M / Kashiwagi K / Ito T | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Elife / Year: 2022 Title: METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance. Authors: Eriko Matsuura-Suzuki / Tadahiro Shimazu / Mari Takahashi / Kaoru Kotoshiba / Takehiro Suzuki / Kazuhiro Kashiwagi / Yoshihiro Sohtome / Mai Akakabe / Mikiko Sodeoka / Naoshi Dohmae / ...Authors: Eriko Matsuura-Suzuki / Tadahiro Shimazu / Mari Takahashi / Kaoru Kotoshiba / Takehiro Suzuki / Kazuhiro Kashiwagi / Yoshihiro Sohtome / Mai Akakabe / Mikiko Sodeoka / Naoshi Dohmae / Takuhiro Ito / Yoichi Shinkai / Shintaro Iwasaki / Abstract: Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a methylation substrate. However, a limited number of enzymes responsible for this modification ...Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a methylation substrate. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood to date. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traversal on Tyr codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ- position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation reactions. Indeed, genome-wide ribosome profiling and an in vitro translation assay revealed that translation elongation at Tyr codons was suppressed by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a ribosome modification that ensures proteome integrity in cells. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31465.map.gz | 109.9 MB | EMDB map data format | |
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Header (meta data) | emd-31465-v30.xml emd-31465.xml | 55.5 KB 55.5 KB | Display Display | EMDB header |
Images | emd_31465.png | 115.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31465 | HTTPS FTP |
-Validation report
Summary document | emd_31465_validation.pdf.gz | 360 KB | Display | EMDB validaton report |
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Full document | emd_31465_full_validation.pdf.gz | 359.6 KB | Display | |
Data in XML | emd_31465_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_31465_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31465 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31465 | HTTPS FTP |
-Related structure data
Related structure data | 7f5sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31465.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : 60S
+Supramolecule #1: 60S
+Macromolecule #1: 60S ribosomal protein L8
+Macromolecule #2: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: 60S ribosomal protein L7
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: 60S ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: 60S ribosomal protein L13a
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L18
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: 60S ribosomal protein L22
+Macromolecule #24: 60S ribosomal protein L23
+Macromolecule #25: 60S ribosomal protein L24
+Macromolecule #26: 60S ribosomal protein L23a
+Macromolecule #27: 60S ribosomal protein L26
+Macromolecule #28: 60S ribosomal protein L27
+Macromolecule #29: 60S ribosomal protein L27a
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L35a
+Macromolecule #35: 60S ribosomal protein L34
+Macromolecule #36: 60S ribosomal protein L35
+Macromolecule #37: 60S ribosomal protein L36
+Macromolecule #38: 60S ribosomal protein L37
+Macromolecule #39: 60S ribosomal protein L38
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L41
+Macromolecule #43: 60S ribosomal protein L36a
+Macromolecule #44: 60S ribosomal protein L37a
+Macromolecule #45: 60S ribosomal protein L28
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #46: MAGNESIUM ION
+Macromolecule #47: ZINC ION
+Macromolecule #48: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118470 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |