2G9N

Structure of the DEAD domain of Human eukaryotic initiation factor 4A, eIF4A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Comparative Structural Analysis of Human DEAD-Box RNA Helicases.

Schutz, P.Karlberg, T.van den Berg, S.Collins, R.Lehtio, L.Hogbom, M.Holmberg-Schiavone, L.Tempel, W.Park, H.W.Hammarstrom, M.Moche, M.Thorsell, A.G.Schuler, H.

(2010) PLoS One 5: 12791-12791

  • DOI: https://doi.org/10.1371/journal.pone.0012791
  • Primary Citation of Related Structures:  
    2G9N, 2P6N, 2PL3, 2RB4, 3B7G, 3BER, 3BOR, 3DKP, 3FE2, 3IUY, 3LY5

  • PubMed Abstract: 

    DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.


  • Organizational Affiliation

    Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-I
A, B
221Homo sapiensMutation(s): 14 
Gene Names: EIF4A1DDX2AEIF4A
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60842 (Homo sapiens)
Explore P60842 
Go to UniProtKB:  P60842
PHAROS:  P60842
GTEx:  ENSG00000161960 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60842
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.799α = 90
b = 78.252β = 103.43
c = 59.088γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description