4XVL

Binary complex of human polymerase nu and DNA with the finger domain open

  • 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: 3.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 nu A666Homo 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
GTEx:  ENSG00000130997
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*G)-3')P14Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-3')T10Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MES
      Query on MES
      Download Ideal Coordinates CCD File 
      A
      		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
      C6 H13 N O4 S
      SXGZJKUKBWWHRA-UHFFFAOYSA-N      		 Ligand Interaction
      NA
      Query on NA
      Download Ideal Coordinates CCD File 
      A
      		SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.30 Å
      • R-Value Free: 0.223 
      • R-Value Work: 0.203 
      • R-Value Observed: 0.204 
      • Space Group: H 3 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 292.125α = 90
      b = 292.125β = 90
      c = 108.14γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      PDB_EXTRACTdata extraction
      HKL-2000data scaling
      MOLREPphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      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
      • Version 2.0: 2019-12-25
        Changes: Atomic model, Author supporting evidence