3VKE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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This is version 1.2 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: https://doi.org/10.1093/nar/gks058
  • Primary Citation of Related Structures:  
    1ZTG, 3VKE

  • 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, 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(rC)-binding protein 1
A, B, C, D
76Homo sapiensMutation(s): 1 
Gene Names: PCBP1
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

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')E [auth R],
F [auth S],
G [auth T],
H [auth U]
6N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.597α = 90
b = 114.887β = 93.73
c = 43.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description