8AVG

Cryo-EM structure of mouse Elp123 with bound SAM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6QK7


Literature

Cryo-EM structure of the fully assembled Elongator complex.

Jaciuk, M.Scherf, D.Kaszuba, K.Gaik, M.Rau, A.Koscielniak, A.Krutyholowa, R.Rawski, M.Indyka, P.Graziadei, A.Chramiec-Glabik, A.Biela, A.Dobosz, D.Lin, T.Y.Abbassi, N.E.Hammermeister, A.Rappsilber, J.Kosinski, J.Schaffrath, R.Glatt, S.

(2023) Nucleic Acids Res 51: 2011-2032

  • DOI: https://doi.org/10.1093/nar/gkac1232
  • Primary Citation of Related Structures:  
    8ASV, 8ASW, 8AT6, 8AVG

  • PubMed Abstract: 

    Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.


  • Organizational Affiliation

    Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 11,333Mus musculusMutation(s): 0 
Gene Names: Elp1IkapIkbkap
UniProt & NIH Common Fund Data Resources
Find proteins for Q7TT37 (Mus musculus)
Explore Q7TT37 
Go to UniProtKB:  Q7TT37
IMPC:  MGI:1914544
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7TT37
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 2831Mus musculusMutation(s): 0 
Gene Names: Elp2Statip1
UniProt
Find proteins for Q91WG4 (Mus musculus)
Explore Q91WG4 
Go to UniProtKB:  Q91WG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91WG4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 3547Mus musculusMutation(s): 0 
Gene Names: Elp3
EC: 2.3.1
UniProt
Find proteins for Q9CZX0 (Mus musculus)
Explore Q9CZX0 
Go to UniProtKB:  Q9CZX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CZX0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2018/31/B/NZ1/03559
European Research Council (ERC)European Union101001394

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references