1ZTG

human alpha polyC binding protein KH1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

Yoga, Y.M.K.Traore, D.A.K.Sidiqi, M.Szeto, C.Pendini, N.R.Barker, A.Leedman, P.J.Wilce, J.A.Wilce, M.C.J.

(2012) Nucleic Acids Res. 40: 5101-5114

  • DOI: 10.1093/nar/gks058
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, ...

    Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA and DNA, KH3 binds with intermediate affinity and KH2 only interacts detectibly with DNA. The crystal structure of KH1 bound to a 5'-CCCTCCCT-3' DNA sequence shows a 2:1 protein:DNA stoichiometry and demonstrates a molecular arrangement of KH domains bound to immediately adjacent oligonucleotide target sites. SPR experiments, with a series of poly-C-sequences reveals that cytosine is preferred at all four positions in the oligonucleotide binding cleft and that a C-tetrad binds KH1 with 10 times higher affinity than a C-triplet. The basis for this high affinity interaction is finally detailed with the structure determination of a KH1.W.C54S mutant bound to 5'-ACCCCA-3' DNA sequence. Together, these data establish the lead role of KH1 in oligonucleotide binding by αCP1 and reveal the molecular basis of its specificity for a C-rich tetrad.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLY(RC)-BINDING PROTEIN 1
A, B, C, D
74Homo sapiensMutation(s): 0 
Gene Names: PCBP1
Find proteins for Q15365 (Homo sapiens)
Go to Gene View: PCBP1
Go to UniProtKB:  Q15365
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*CP*CP*TP*CP*CP*CP*T)-3'Y,Z8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.600α = 90.00
b = 76.800β = 111.70
c = 61.400γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-27
    Type: Initial release
  • Version 1.1: 2008-12-04
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2012-03-07
    Type: Database references
  • Version 1.4: 2013-07-17
    Type: Database references