4EJS

Structure of yeast elongator subcomplex Elp456


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of elongator subcomplex Elp4-6

Lin, Z.Zhao, W.Diao, W.Xie, X.Wang, Z.Zhang, J.Shen, Y.Long, J.

(2012) J Biol Chem 287: 21501-21508

  • DOI: https://doi.org/10.1074/jbc.M112.341560
  • Primary Citation of Related Structures:  
    4EJS

  • PubMed Abstract: 

    Elongator is a multiprotein complex composed of two subcomplexes, Elp1-3 and Elp4-6. Elongator is highly conserved between yeast and humans and plays an important role in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. Here, we determined the crystal structure of the Elp4-6 subcomplex of yeast. The overall structure of Elp4-6 revealed that Elp6 acts as a bridge to assemble Elp4 and Elp5. Detailed structural and sequence analyses revealed that each subunit in the Elp4-6 subcomplex forms a RecA-ATPase-like fold, although it lacks the key sequence signature of ATPases. Site-directed mutagenesis and biochemical analyses indicated that the Elp4-6 subcomplex can assemble into a hexameric ring-shaped structure in vitro and in vivo. Furthermore, GST pulldown assays showed that the ring-shaped assembly of the Elp4-6 subcomplex is important for its specific histone H3 binding. Our results may shed light on the substrate recognition and assembly of the holo-Elongator complex.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 4376Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ELP4
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 5242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ELP5
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 6277Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ELP6
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.513α = 90
b = 186.513β = 90
c = 186.513γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references