1UL1 | pdb_00001ul1

Crystal structure of the human FEN1-PCNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.284 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.219 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1UL1

This is version 1.4 of the entry. See complete history

Literature

Structural basis for recruitment of human flap endonuclease 1 to PCNA

Sakurai, S.Kitano, K.Yamaguchi, H.Okada, K.Hamada, K.Fukuda, K.Uchida, M.Ohtsuka, E.Morioka, H.Hakoshima, T.

(2005) EMBO J 24: 683-693

  • DOI: https://doi.org/10.1038/sj.emboj.7600519
  • Primary Citation Related Structures: 
    1UL1

  • PubMed Abstract: 

    Flap endonuclease-1 (FEN1) is a key enzyme for maintaining genomic stability and replication. Proliferating cell nuclear antigen (PCNA) binds FEN1 and stimulates its endonuclease activity. The structural basis of the FEN1-PCNA interaction was revealed by the crystal structure of the complex between human FEN1 and PCNA. The main interface involves the C-terminal tail of FEN1, which forms two beta-strands connected by a short helix, the betaA-alphaA-betaB motif, participating in beta-beta and hydrophobic interactions with PCNA. These interactions are similar to those previously observed for the p21CIP1/WAF1 peptide. However, this structure involving the full-length enzyme has revealed additional interfaces that are involved in the core domain. The interactions at the interfaces maintain the enzyme in an inactive 'locked-down' orientation and might be utilized in rapid DNA-tracking by preserving the central hole of PCNA for sliding along the DNA. A hinge region present between the core domain and the C-terminal tail of FEN1 would play a role in switching the FEN1 orientation from an inactive to an active orientation.


  • Organizational Affiliation
    • Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan.

Macromolecule Content 

  • Total Structure Weight: 214.07 kDa 
  • Atom Count: 13,162 
  • Modeled Residue Count: 1,743 
  • Deposited Residue Count: 1,920 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Flap endonuclease-1A [auth X],
B [auth Y],
C [auth Z]
379Homo sapiensMutation(s): 0 
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P39748 (Homo sapiens)
Explore P39748 
Go to UniProtKB:  P39748
PHAROS:  P39748
GTEx:  ENSG00000168496 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39748
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenD [auth A],
E [auth B],
F [auth C]
261Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
PHAROS:  P12004
GTEx:  ENSG00000132646 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12004
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.284 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.219 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.203α = 90
b = 143.383β = 90
c = 246.659γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2007-10-23
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Structure summary