1WVN

Crystal Structure of domain 3 of human alpha polyC binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure and RNA binding of the third KH domain of poly(C)-binding protein 1.

Sidiqi, M.Wilce, J.A.Vivian, J.P.Porter, C.J.Barker, A.Leedman, P.J.Wilce, M.C.J.

(2005) Nucleic Acids Res 33: 1213-1221

  • DOI: https://doi.org/10.1093/nar/gki265
  • Primary Citation of Related Structures:  
    1WVN

  • PubMed Abstract: 

    Poly(C)-binding proteins (CPs) are important regulators of mRNA stability and translational regulation. They recognize C-rich RNA through their triple KH (hn RNP K homology) domain structures and are thought to carry out their function though direct protection of mRNA sites as well as through interactions with other RNA-binding proteins. We report the crystallographically derived structure of the third domain of alphaCP1 to 2.1 A resolution. alphaCP1-KH3 assumes a classical type I KH domain fold with a triple-stranded beta-sheet held against a three-helix cluster in a betaalphaalphabetabetaalpha configuration. Its binding affinity to an RNA sequence from the 3'-untranslated region (3'-UTR) of androgen receptor mRNA was determined using surface plasmon resonance, giving a K(d) of 4.37 microM, which is indicative of intermediate binding. A model of alphaCP1-KH3 with poly(C)-RNA was generated by homology to a recently reported RNA-bound KH domain structure and suggests the molecular basis for oligonucleotide binding and poly(C)-RNA specificity.


  • Organizational Affiliation

    School of Biomedical and Chemical Sciences, the UWA Centre for Medical Research, The University of Western Australia WA Australia 6009.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(rC)-binding protein 182Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15365 (Homo sapiens)
Explore Q15365 
Go to UniProtKB:  Q15365
PHAROS:  Q15365
GTEx:  ENSG00000169564 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15365
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.4α = 90
b = 71β = 90
c = 29.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-01-23
    Changes: Data collection, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Refinement description