3KTR

Structural basis of ataxin-2 recognition by poly(A)-binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of binding of P-body-associated proteins GW182 and ataxin-2 by the Mlle domain of poly(A)-binding protein.

Kozlov, G.Safaee, N.Rosenauer, A.Gehring, K.

(2010) J Biol Chem 285: 13599-13606

  • DOI: 10.1074/jbc.M109.089540
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Poly(A)-binding protein (PABPC1) is involved in multiple aspects of mRNA processing and translation. It is a component of RNA stress granules and binds the RNA-induced silencing complex to promote degradation of silenced mRNAs. Here, we report the cr ...

    Poly(A)-binding protein (PABPC1) is involved in multiple aspects of mRNA processing and translation. It is a component of RNA stress granules and binds the RNA-induced silencing complex to promote degradation of silenced mRNAs. Here, we report the crystal structures of the C-terminal Mlle (or PABC) domain in complex with peptides from GW182 (TNRC6C) and Ataxin-2. The structures reveal overlapping binding sites but with unexpected diversity in the peptide conformation and residues involved in binding. The mutagenesis and binding studies show low to submicromolar binding affinity with overlapping but distinct specificity determinants. These results rationalize the role of the Mlle domain of PABPC1 in microRNA-mediated mRNA deadenylation and suggest a more general function in the assembly of cytoplasmic RNA granules.


    Organizational Affiliation

    Department of Biochemistry and Groupe de Recherche axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G1Y6, Canada.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyadenylate-binding protein 1A88Homo sapiensMutation(s): 0 
Gene Names: PABPC1PAB1PABP1PABPC2
Find proteins for P11940 (Homo sapiens)
Explore P11940 
Go to UniProtKB:  P11940
NIH Common Fund Data Resources
PHAROS  P11940
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ataxin-2B17Homo sapiensMutation(s): 0 
Gene Names: ATXN2ATX2SCA2TNRC13
Find proteins for Q99700 (Homo sapiens)
Explore Q99700 
Go to UniProtKB:  Q99700
NIH Common Fund Data Resources
PHAROS  Q99700
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.093α = 90
b = 60.745β = 90
c = 31.52γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance