7KQ0

PCNA bound to peptide mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unlocking the PIP-box: A peptide library reveals interactions that drive high-affinity binding to human PCNA.

Horsfall, A.J.Vandborg, B.A.Kowalczyk, W.Chav, T.Scanlon, D.B.Abell, A.D.Bruning, J.B.

(2021) J Biol Chem 296: 100773-100773

  • DOI: 10.1016/j.jbc.2021.100773
  • Primary Citation of Related Structures:  
    7KQ0, 7KQ1

  • PubMed Abstract: 
  • The human sliding clamp, Proliferating Cell Nuclear Antigen (hPCNA), interacts with over 200 proteins through a conserved binding motif, the PIP-box, to orchestrate DNA replication and repair. It is not clear how changes to the features of a PIP-box modulate protein binding and thus how they fine-tune downstream processes ...

    The human sliding clamp, Proliferating Cell Nuclear Antigen (hPCNA), interacts with over 200 proteins through a conserved binding motif, the PIP-box, to orchestrate DNA replication and repair. It is not clear how changes to the features of a PIP-box modulate protein binding and thus how they fine-tune downstream processes. Here, we present a systematic study of each position within the PIP-box to reveal how hPCNA-interacting peptides bind with drastically varied affinities. We synthesized a series of 27 peptides derived from the native protein p21 with small PIP-box modifications and another series of 19 peptides containing PIP-box binding motifs from other proteins. The hPCNA-binding affinity of all peptides, characterized as K D values determined by surface plasmon resonance, spanned a 4000-fold range, from 1.83 nM to 7.59 μM. The hPCNA-bound peptide structures determined by X-ray crystallography and modeled computationally revealed intermolecular and intramolecular interaction networks that correlate with high hPCNA affinity. These data informed rational design of three new PIP-box sequences, testing of which revealed the highest affinity hPCNA-binding partner to date, with a K D value of 1.12 nM, from a peptide with PIP-box QTRITEYF. This work showcases the sequence-specific nuances within the PIP-box that are responsible for high-affinity hPCNA binding, which underpins our understanding of how nature tunes hPCNA affinity to regulate DNA replication and repair processes. In addition, these insights will be useful to future design of hPCNA inhibitors.


    Organizational Affiliation

    Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia. Electronic address: john.bruning@adelaide.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenA, C, E259Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
PHAROS:  P12004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12004
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARGB, D, F15synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P38936 (Homo sapiens)
Explore P38936 
Go to UniProtKB:  P38936
PHAROS:  P38936
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38936
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.164 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.563α = 90
b = 142.563β = 90
c = 41.03γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references