4XVM

Binary complex of human polymerase nu and DNA with the finger domain closed and thumb domain rotated out

  • Classification: TRANSFERASE/DNA
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2015-01-27 Released: 2015-03-11 
  • Deposition Author(s): Lee, Y.-S., Yang, W.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis.

Lee, Y.S.Gao, Y.Yang, W.

(2015) Nat Struct Mol Biol 22: 298-303

  • DOI: 10.1038/nsmb.2985
  • Primary Citation of Related Structures:  
    4XVK, 4XVL, 4XVM, 4XVI

  • PubMed Abstract: 
  • All DNA replicases achieve high fidelity by a conserved mechanism, but each translesion polymerase carries out mutagenic DNA synthesis in its own way. Here we report crystal structures of human DNA polymerase ν (Pol ν), which is homologous to high-fidelity replicases yet is error prone ...

    All DNA replicases achieve high fidelity by a conserved mechanism, but each translesion polymerase carries out mutagenic DNA synthesis in its own way. Here we report crystal structures of human DNA polymerase ν (Pol ν), which is homologous to high-fidelity replicases yet is error prone. Instead of a simple open-to-closed movement of the O helix upon binding of a correct incoming nucleotide, Pol ν has a different open state and requires the finger domain to swing sideways and undergo both opening and closing motions to accommodate the nascent base pair. A single-amino acid substitution in the O helix of the finger domain improves the fidelity of Pol ν nearly ten-fold. A unique cavity and the flexibility of the thumb domain allow Pol ν to generate and accommodate a looped-out primer strand. Primer loop-out may be a mechanism for DNA trinucloetide-repeat expansion.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase nuA666Homo sapiensMutation(s): 0 
Gene Names: POLN
EC: 2.7.7.7
Find proteins for Q7Z5Q5 (Homo sapiens)
Explore Q7Z5Q5 
Go to UniProtKB:  Q7Z5Q5
NIH Common Fund Data Resources
PHAROS:  Q7Z5Q5
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*AP*GP*CP*GP*TP*CP*A)-3')B [auth T]9Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*G)-3')C [auth P]13Homo sapiens
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Free: 0.281 
      • R-Value Work: 0.242 
      • R-Value Observed: 0.244 
      • Space Group: I 2 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 97.995α = 90
      b = 110.924β = 90
      c = 277.418γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data reduction
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data scaling
      MOLREPphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2015-01-27 
      • Released Date: 2015-03-11 
      • Deposition Author(s): Lee, Y.-S., Yang, W.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK036146-08

      Revision History  (Full details and data files)

      • Version 1.0: 2015-03-11
        Type: Initial release
      • Version 1.1: 2015-04-01
        Changes: Database references
      • Version 1.2: 2015-04-15
        Changes: Database references
      • Version 1.3: 2017-09-27
        Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
      • Version 1.4: 2019-12-25
        Changes: Author supporting evidence