4RI8

FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1.

Wang, R.Persky, N.S.Yoo, B.Ouerfelli, O.Smogorzewska, A.Elledge, S.J.Pavletich, N.P.

(2014) Science 346: 1127-1130

  • DOI: 10.1126/science.1258973
  • Primary Citation of Related Structures:  
    4RIC, 4RID, 4RIA, 4RIB, 4RI8, 4RI9

  • PubMed Abstract: 
  • DNA interstrand cross-links (ICLs) are highly toxic lesions associated with cancer and degenerative diseases. ICLs can be repaired by the Fanconi anemia (FA) pathway and through FA-independent processes involving the FAN1 nuclease. In this work, FAN1-DNA crystal structures and biochemical data reveal that human FAN1 cleaves DNA successively at every third nucleotide ...

    DNA interstrand cross-links (ICLs) are highly toxic lesions associated with cancer and degenerative diseases. ICLs can be repaired by the Fanconi anemia (FA) pathway and through FA-independent processes involving the FAN1 nuclease. In this work, FAN1-DNA crystal structures and biochemical data reveal that human FAN1 cleaves DNA successively at every third nucleotide. In vitro, this exonuclease mechanism allows FAN1 to excise an ICL from one strand through flanking incisions. DNA access requires a 5'-terminal phosphate anchor at a nick or a 1- or 2-nucleotide flap and is augmented by a 3' flap, suggesting that FAN1 action is coupled to DNA synthesis or recombination. FAN1's mechanism of ICL excision is well suited for processing other localized DNA adducts as well.


    Organizational Affiliation

    Structural Biology Program and Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. pavletin@mskcc.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fanconi-associated nuclease 1 AB651Homo sapiensMutation(s): 1 
Gene Names: FAN1KIAA1018MTMR15
EC: 3.1.21 (PDB Primary Data), 3.1.4.1 (PDB Primary Data)
Find proteins for Q9Y2M0 (Homo sapiens)
Explore Q9Y2M0 
Go to UniProtKB:  Q9Y2M0
NIH Common Fund Data Resources
PHAROS:  Q9Y2M0
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')E, H14N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')F, I8N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')G, J19N/A
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        CA
        Query on CA

        Download Ideal Coordinates CCD File 
        A, B
        CALCIUM ION
        Ca
        BHPQYMZQTOCNFJ-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.90 Å
        • R-Value Free: 0.255 
        • R-Value Work: 0.221 
        • R-Value Observed: 0.222 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 62.26α = 90
        b = 210.88β = 107.61
        c = 83.22γ = 90
        Software Package:
        Software NamePurpose
        SCALEPACKdata scaling
        REFMACrefinement
        PDB_EXTRACTdata extraction
        ADSCdata collection
        DENZOdata reduction
        SHARPphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2014-12-03
          Type: Initial release
        • Version 1.1: 2014-12-10
          Changes: Database references