4F02

Crystal structure of the PABP-binding site of eIF4G in complex with RRM1-2 of PABP and poly(A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interdomain Allostery Promotes Assembly of the Poly(A) mRNA Complex with PABP and eIF4G.

Safaee, N.Kozlov, G.Noronha, A.M.Xie, J.Wilds, C.J.Gehring, K.

(2012) Mol Cell 48: 375-386

  • DOI: 10.1016/j.molcel.2012.09.001
  • Primary Citation of Related Structures:  
    4F02, 4F25, 4F26

  • PubMed Abstract: 
  • Many RNA-binding proteins contain multiple single-strand nucleic acid-binding domains and assemble into large multiprotein messenger ribonucleic acid protein (mRNP) complexes. The mechanisms underlying the self-assembly of these complexes are largely unknown ...

    Many RNA-binding proteins contain multiple single-strand nucleic acid-binding domains and assemble into large multiprotein messenger ribonucleic acid protein (mRNP) complexes. The mechanisms underlying the self-assembly of these complexes are largely unknown. In eukaryotes, the association of the translation factors polyadenylate-binding protein-1 (PABP) and eIF4G is essential for high-level expression of polyadenylated mRNAs. Here, we report the crystal structure of the ternary complex poly(A)(11)·PABP(1-190)·eIF4G(178-203) at 2.0 Å resolution. Our NMR and crystallographic data show that eIF4G interacts with the RRM2 domain of PABP. Analysis of the interaction by small-angle X-ray scattering, isothermal titration calorimetry, and electromobility shift assays reveals that this interaction is allosterically regulated by poly(A) binding to PABP. Furthermore, we have confirmed the importance of poly(A) for the endogenous PABP and eIF4G interaction in immunoprecipitation experiments using HeLa cell extracts. Our findings reveal interdomain allostery as a mechanism for cooperative assembly of RNP complexes.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyadenylate-binding protein 1A, D213Homo sapiensMutation(s): 0 
Gene Names: PABPC1PAB1PABP1PABPC2
UniProt & NIH Common Fund Data Resources
Find proteins for P11940 (Homo sapiens)
Explore P11940 
Go to UniProtKB:  P11940
PHAROS:  P11940
Entity Groups  
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UniProt GroupP11940
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4 gamma 1C, F27Homo sapiensMutation(s): 0 
Gene Names: EIF4G1EIF4FEIF4GEIF4GI
UniProt & NIH Common Fund Data Resources
Find proteins for Q04637 (Homo sapiens)
Explore Q04637 
Go to UniProtKB:  Q04637
PHAROS:  Q04637
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04637
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')B, E 11N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.191α = 90
b = 130.191β = 90
c = 86.872γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description