4RIA

FAN1 Nuclease bound to 5' phosphorylated nicked DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 A, B651Homo sapiensMutation(s): 1 
Gene Names: FAN1, KIAA1018, MTMR15
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
GTEx:  ENSG00000198690
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')F, L10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')I, K9N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')G, J14N/A
        • Find similar nucleic acids by:  Sequence   |   Structure
          • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')E, H12N/A
          Small Molecules
          Ligands 1 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          BA
          Query on BA
          Download Ideal Coordinates CCD File 
          A, B
          		BARIUM ION
          Ba
          XDFCIPNJCBUZJN-UHFFFAOYSA-N          		 Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.00 Å
          • R-Value Free: 0.267 
          • R-Value Work: 0.224 
          • R-Value Observed: 0.226 
          • Space Group: P 2 21 21
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 87.813α = 90
          b = 100.317β = 90
          c = 212.465γ = 90
          Software Package:
          Software NamePurpose
          SCALEPACKdata scaling
          REFMACrefinement
          PDB_EXTRACTdata extraction
          ADSCdata collection
          DENZOdata reduction
          SHARPphasing

          Structure Validation

          View Full Validation Report


          View more in-depth experimental data

          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2014-12-10
            Type: Initial release