5M2N

Crystal Structure of Elongator subunit Elp2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Architecture of the yeast Elongator complex.

Dauden, M.I.Kosinski, J.Kolaj-Robin, O.Desfosses, A.Ori, A.Faux, C.Hoffmann, N.A.Onuma, O.F.Breunig, K.D.Beck, M.Sachse, C.Seraphin, B.Glatt, S.Muller, C.W.

(2017) EMBO Rep 18: 264-279

  • DOI: https://doi.org/10.15252/embr.201643353
  • Primary Citation of Related Structures:  
    5M2N

  • PubMed Abstract: 

    The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
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
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.69α = 90
b = 79.69β = 90
c = 532.15γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyBR921/9-1
German Research FoundationGermanyMu3173/2-1
National Science CentrePoland2015/19/B/NZ1/00343

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary