4A8J | pdb_00004a8j

Crystal Structure of the Elongator subcomplex Elp456


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.201 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8ASV 8AT6

Literature

The Elongator Subcomplex Elp456 is a Hexameric Reca-Like ATPase.

Glatt, S.Letoquart, J.Faux, C.Taylor, N.M.I.Seraphin, B.Muller, C.W.

(2012) Nat Struct Mol Biol 19: 314

  • DOI: https://doi.org/10.1038/nsmb.2234
  • Primary Citation Related Structures: 
    4A8J

  • PubMed Abstract: 

    Elongator was initially described as an RNA polymerase II-associated factor but has since been associated with a broad range of cellular activities. It has also attracted clinical attention because of its role in certain neurodegenerative diseases. Here we describe the crystal structure of the Saccharomyces cerevisiae subcomplex of Elongator proteins 4, 5 and 6 (Elp456). The subunits each show almost identical RecA folds that form a heterohexameric ring-like structure resembling hexameric RecA-like ATPases. This structural finding is supported by different complementary in vitro and in vivo approaches, including the specific binding of the hexameric Elp456 subcomplex to tRNAs in a manner regulated by ATP. Our results support a role of Elongator in tRNA modification, explain the importance of each of the Elp4, Elp5 and Elp6 subunits for complex integrity and suggest a model for the overall architecture of the holo-Elongator complex.


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

Macromolecule Content 

  • Total Structure Weight: 208.34 kDa 
  • Atom Count: 13,005 
  • Modeled Residue Count: 1,523 
  • Deposited Residue Count: 1,822 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongator complex protein 4
A, D
361Saccharomyces cerevisiae S288CMutation(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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongator complex protein 5
B, E
270Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IKI1ELP5HAP2TOT5YHR187W
UniProt
Find proteins for P38874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38874 
Go to UniProtKB:  P38874
Entity Groups
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UniProt GroupP38874
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongator complex protein 6
C, F
280Saccharomyces cerevisiae S288CMutation(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
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.201 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.73α = 90
b = 124.89β = 90
c = 146.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Other
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Other
  • Version 1.3: 2024-09-11
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2024-10-23
    Changes: Structure summary