2J0U | pdb_00002j0u

The crystal structure of eIF4AIII-Barentsz complex at 3.0 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.328 (Depositor), 0.348 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.298 (DCC) 
  • R-Value Observed: 
    0.276 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of the Exon Junction Complex Reveals How It Mantains a Stable Grip on Mrna

Bono, F.Ebert, J.Lorentzen, E.Conti, E.

(2006) Cell 126: 713

  • DOI: https://doi.org/10.1016/j.cell.2006.08.006
  • Primary Citation Related Structures: 
    2J0Q, 2J0S, 2J0U

  • PubMed Abstract: 

    The exon junction complex (EJC) plays a major role in posttranscriptional regulation of mRNA in metazoa. The EJC is deposited onto mRNA during splicing and is transported to the cytoplasm where it influences translation, surveillance, and localization of the spliced mRNA. The complex is formed by the association of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. The 2.2 A resolution structure of the EJC reveals how it stably locks onto mRNA. The DEAD-box protein eIF4AIII encloses an ATP molecule and provides the binding sites for six ribonucleotides. Btz wraps around eIF4AIII and stacks against the 5' nucleotide. An intertwined network of interactions anchors Mago-Y14 and Btz at the interface between the two domains of eIF4AIII, effectively stabilizing the ATP bound state. Comparison with the structure of the eIF4AIII-Btz subcomplex that we have also determined reveals that large conformational changes are required upon EJC assembly and disassembly.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 98.91 kDa 
  • Atom Count: 5,139 
  • Modeled Residue Count: 722 
  • Deposited Residue Count: 862 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-DEPENDENT RNA HELICASE DDX48374Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P38919 (Homo sapiens)
Explore P38919 
Go to UniProtKB:  P38919
PHAROS:  P38919
GTEx:  ENSG00000141543 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38919
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-DEPENDENT RNA HELICASE DDX48374Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P38919 (Homo sapiens)
Explore P38919 
Go to UniProtKB:  P38919
PHAROS:  P38919
GTEx:  ENSG00000141543 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38919
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN CASC3C [auth T]114Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15234 (Homo sapiens)
Explore O15234 
Go to UniProtKB:  O15234
PHAROS:  O15234
GTEx:  ENSG00000108349 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15234
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.328 (Depositor), 0.348 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.298 (DCC) 
  • R-Value Observed: 0.276 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.76α = 90
b = 107.19β = 90
c = 243.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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: 2006-09-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description