6W0R

Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report



Literature

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.

Shigdel, U.K.Ovchinnikov, V.Lee, S.J.Shih, J.A.Karplus, M.Nam, K.Verdine, G.L.

(2020) Nat Commun 11: 4437-4437

  • DOI: 10.1038/s41467-020-18290-2
  • Primary Citation of Related Structures:  
    6W0M, 6W0R, 6W13

  • PubMed Abstract: 
  • Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the D ...

    Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA. Gregory_verdine@harvard.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-glycosylase/DNA lyaseA315Homo sapiensMutation(s): 2 
Gene Names: OGG1MMHMUTMOGH1
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for O15527 (Homo sapiens)
Explore O15527 
Go to UniProtKB:  O15527
NIH Common Fund Data Resources
PHAROS  O15527
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*AP*GP*GP*TP*C)-3')B6Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*CP*TP*GP*G)-3')C5Homo sapiens
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      S5Y
      Query on S5Y

      Download CCD File 
      B
      2-(2-ethoxyethoxy)ethanethiol
      C6 H14 O2 S
      LIAMZAFGRCLLJR-UHFFFAOYSA-N
       Ligand Interaction
      NO3
      Query on NO3

      Download CCD File 
      A
      NITRATE ION
      N O3
      NHNBFGGVMKEFGY-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

      Download CCD File 
      A
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.35 Å
      • R-Value Free: 0.249 
      • R-Value Work: 0.208 
      • R-Value Observed: 0.210 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 88.928α = 90
      b = 88.928β = 90
      c = 210.539γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      HKL-2000data reduction
      PDB_EXTRACTdata extraction
      PHASERphasing
      HKL-2000data processing
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

      Revision History 

      • Version 1.0: 2020-09-23
        Type: Initial release