8ASV

Cryo-EM structure of yeast Elongator complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.35 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 4A8J


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 1
A, D
1,349Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IKI3ELP1TOT1YLR384CL3502.7
UniProt
Find proteins for Q06706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06706 
Go to UniProtKB:  Q06706
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06706
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 2788Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ELP2TOT2YGR200CG7725
UniProt
Find proteins for P42935 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P42935 
Go to UniProtKB:  P42935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42935
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 3557Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ELP3HPA1TOT3YPL086C
EC: 2.3.1
UniProt
Find proteins for Q02908 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02908 
Go to UniProtKB:  Q02908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02908
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 5
E, H
309Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IKI1ELP5HAP2TOT5YHR187W
UniProt
Find proteins for P38874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38874 
Go to UniProtKB:  P38874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38874
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 6
F, I
273Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ELP6HAP3TOT6YMR312WYM9924.04
UniProt
Find proteins for Q04868 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04868 
Go to UniProtKB:  Q04868
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04868
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 4
G, J
456Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ELP4HAP1TOT7YPL101W
UniProt
Find proteins for Q02884 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02884 
Go to UniProtKB:  Q02884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02884
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
K [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.35 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