5IY4

Crystal structure of human PCNA in complex with the PIP box of DVC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.945 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human PCNA in complex with the PIP box of DVC1

Wang, Y.Xu, M.Jiang, T.

(2016) Biochem.Biophys.Res.Commun. 474: 264-270

  • DOI: 10.1016/j.bbrc.2016.04.053

  • PubMed Abstract: 
  • In higher eukaryotes, DVC1 (SPRTN, Spartan or C1orf124) is implicated in the translesion synthesis (TLS) pathway. DVC1 localizes to sites of DNA damage, binds to the proliferating cell nuclear antigen (PCNA) via its conserved PCNA-interacting motif ( ...

    In higher eukaryotes, DVC1 (SPRTN, Spartan or C1orf124) is implicated in the translesion synthesis (TLS) pathway. DVC1 localizes to sites of DNA damage, binds to the proliferating cell nuclear antigen (PCNA) via its conserved PCNA-interacting motif (PIP box), and associates with ubiquitin selective segregase p97 and other factors, thus regulating translesion synthesis polymerases. Here, we report the crystal structure of human PCNA in complex with a peptide ((321)SNSHQNVLSNYFPRVS(336)) derived from human DVC1 that contains a unique YF type PIP box. Structural analysis reveals the detailed PIP box-PCNA interaction. Interestingly, substitution of Y331 with Phe severely reduces its PCNA binding affinity. These findings offer new insights into the determinants of PIP box for PCNA binding.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C, E
270Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DVC1 PIP box
B, D, F
16Homo sapiensMutation(s): 0 
Gene Names: SPRTN (C1orf124, DVC1)
Find proteins for Q9H040 (Homo sapiens)
Go to Gene View: SPRTN
Go to UniProtKB:  Q9H040
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.945 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.207 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.647α = 90.00
b = 71.647β = 90.00
c = 322.208γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Strategic Priority Research ProgramChinaXDB08010301

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection, Derived calculations