4RIC

FAN1 Nuclease bound to 5' hydroxyl (dT-dT) single flap DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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 AB631Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')U, X21N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')V, Y12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')T, W14N/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: 2.80 Å
      • R-Value Free: 0.257 
      • R-Value Work: 0.223 
      • R-Value Observed: 0.224 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 97.697α = 90
      b = 110.989β = 103.75
      c = 105.427γ = 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