5E0U

Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.

Duffy, C.M., Hilbert, B.J., Kelch, B.A.

(2016) J Mol Biol 428: 1023-1040

  • DOI: 10.1016/j.jmb.2015.11.029
  • Primary Citation of Related Structures:  
    5E0T, 5E0U, 5E0V

  • PubMed Abstract: 

    • The eukaryotic DNA polymerase sliding clamp, proliferating cell nuclear antigen or PCNA, is a ring-shaped protein complex that surrounds DNA to act as a sliding platform for increasing processivity of cellular replicases and for coordinating various cellular pathways with DNA replication ...

    The eukaryotic DNA polymerase sliding clamp, proliferating cell nuclear antigen or PCNA, is a ring-shaped protein complex that surrounds DNA to act as a sliding platform for increasing processivity of cellular replicases and for coordinating various cellular pathways with DNA replication. A single point mutation, Ser228Ile, in the human PCNA gene was recently identified to cause a disease whose symptoms resemble those of DNA damage and repair disorders. The mutation lies near the binding site for most PCNA-interacting proteins. However, the structural consequences of the S228I mutation are unknown. Here, we describe the structure of the disease-causing variant, which reveals a large conformational change that dramatically transforms the binding pocket for PCNA client proteins. We show that the mutation markedly alters the binding energetics for some client proteins, while another, p21(CIP1), is only mildly affected. Structures of the disease variant bound to peptides derived from two PCNA partner proteins reveal that the binding pocket can adjust conformation to accommodate some ligands, indicating that the binding site is dynamic and pliable. Our work has implications for the plasticity of the binding site in PCNA and reveals how a disease mutation selectively alters interactions to a promiscuous binding site that is critical for DNA metabolism.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenA, B, C261Homo sapiensMutation(s): 1 
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
Cyclin-dependent kinase inhibitor 1D, E, F23Homo sapiensMutation(s): 0 
Gene Names: CDKN1A, CAP20, CDKN1, CIP1, MDA6, PIC1, SDI1, WAF1
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: 1.93 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.170 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.295α = 90
b = 143.295β = 90
c = 41.402γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000phasing
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description