[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitlemRNA decoding in human is kinetically and structurally distinct from bacteria.
Journal, issue, pagesNature, Vol. 617, Issue 7959, Page 200-207, Year 2023
Publish dateApr 5, 2023
AuthorsMikael Holm / S Kundhavai Natchiar / Emily J Rundlet / Alexander G Myasnikov / Zoe L Watson / Roger B Altman / Hao-Yuan Wang / Jack Taunton / Scott C Blanchard /
PubMed AbstractIn all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives ...In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems. Although key features are conserved across evolution, eukaryotes achieve higher-fidelity mRNA decoding than bacteria. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.
External linksNature / PubMed:37020024 / PubMed Central
MethodsEM (single particle)
Resolution1.67 - 2.94 Å
Structure data

29757

8g5y

EMDB-29757, PDB-8g5y:
mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)
Method: EM (single particle) / Resolution: 2.29 Å

29758

8g5z

EMDB-29758, PDB-8g5z:
mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)
Method: EM (single particle) / Resolution: 2.64 Å

29759

8g60

EMDB-29759, PDB-8g60:
mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)
Method: EM (single particle) / Resolution: 2.54 Å

29760

8g61

EMDB-29760, PDB-8g61:
mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state)
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-29766: mRNA decoding in human is kinetically and structurally distinct from bacteria (60S Focus refined map)
Method: EM (single particle) / Resolution: 1.7 Å

EMDB-29768: mRNA decoding in human is kinetically and structurally distinct from bacteria (40S Focus refined map)
Method: EM (single particle) / Resolution: 1.8 Å

29771

8g6j

EMDB-29771, PDB-8g6j:
mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-29782: mRNA decoding in human is kinetically and structurally distinct from bacteria (80S consensus refined structure)
Method: EM (single particle) / Resolution: 2.1 Å

40205

8glp

EMDB-40205, PDB-8glp:
mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)
Method: EM (single particle) / Resolution: 1.67 Å

Chemicals

ChemComp-SPD:
SPERMIDINE

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-K:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-ANM:
ANISOMYCIN / antibiotic*YM

ChemComp-3H3:
4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione

ChemComp-ZN:
Unknown entry

ChemComp-MET:
METHIONINE

ChemComp-HOH:
WATER

ChemComp-PHE:
PHENYLALANINE

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

ChemComp-ZIY:
plitidepsin

ChemComp-3HE:
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione

ChemComp-HMT:
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine / anticancer, alkaloid*YM

ChemComp-YRB:
(3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)-1-hydroxy-2-methylpropyl]-8,9,11,17,18-pentamethyl-15-[(2S)-2-methylbutyl]hexadecahydropyrido[1,2-a][1,4,7,10,13,16,19]heptaazacyclohenicosine-1,4,7,10,13,16,19(21H)-heptone

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

Source
  • homo sapiens (human)
  • escherichia coli (E. coli)
KeywordsRIBOSOME / Human 80S / tRNA / mRNA eEF1A / eIF5A / tRNA selection / mRNA tRNA selection

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more