5L7L | pdb_00005l7l

Crystal Structure of Elp3 from Dehalococcoides mccartyi (390-407 GSGSG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5L7L

This is version 1.3 of the entry. See complete history

Literature

Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi.

Glatt, S.Zabel, R.Kolaj-Robin, O.Onuma, O.F.Baudin, F.Graziadei, A.Taverniti, V.Lin, T.Y.Baymann, F.Seraphin, B.Breunig, K.D.Muller, C.W.

(2016) Nat Struct Mol Biol 23: 794-802

  • DOI: https://doi.org/10.1038/nsmb.3265
  • Primary Citation Related Structures: 
    5L7J, 5L7L

  • PubMed Abstract: 

    During translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Mutations in Elongator subunits are associated with certain neurodegenerative diseases and cancer. Here we present the crystal structure of D. mccartyi Elp3 (DmcElp3) at 2.15-Å resolution. Our results reveal an unexpected arrangement of Elp3 lysine acetyltransferase (KAT) and radical S-adenosyl methionine (SAM) domains, which share a large interface and form a composite active site and tRNA-binding pocket, with an iron-sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirmed the relevance of our findings for eukaryotic Elp3s and should aid in understanding the cellular functions and pathophysiological roles of Elongator.


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

Macromolecule Content 

  • Total Structure Weight: 49.88 kDa 
  • Atom Count: 3,081 
  • Modeled Residue Count: 396 
  • Deposited Residue Count: 446 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ELP3 family, ELP3 family446Dehalococcoides mccartyi BTF08Mutation(s): 0 
Gene Names: btf_573
EC: 2.3.1.311
UniProt
Find proteins for A0A1C7D1B7 (Dehalococcoides mccartyi (strain CBDB1))
Explore A0A1C7D1B7 
Go to UniProtKB:  A0A1C7D1B7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1B7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.76α = 90
b = 161.41β = 90
c = 93.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-09-21
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description