5M2N

Crystal Structure of Elongator subunit Elp2

• PDB DOI: https://doi.org/10.2210/pdb5M2N/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-13 Released: 2016-12-28 
• Deposition Author(s): Glatt, S., Mueller, C.W.
• Funding Organization(s): German Research Foundation, National Science Centre

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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 

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

• PubMed: 27974378 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.13 kDa 
• Atom Count: 5,763 
• Modelled Residue Count: 711 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 2	A	788	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ELP2, TOT2, YGR200C, G7725
UniProt
Find proteins for P42935 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42935  Go to UniProtKB:  P42935

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 79.69	α = 90
b = 79.69	β = 90
c = 532.15	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Glatt, S., Mueller, C.W.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	BR921/9-1
German Research Foundation	Germany	Mu3173/2-1
National Science Centre	Poland	2015/19/B/NZ1/00343

Revision History  

• 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