6W0M

Human 8-oxoguanine glycosylase crosslinked with oxoG lesion containing DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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 lyaseA317Homo sapiensMutation(s): 3 
Gene Names: OGG1, MMH, MUTM, OGH1
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
GTEx  ENSG00000114026
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*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')B13Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')C15Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      S5Y
      Query on S5Y
      Download CCD File 
      A
      		2-(2-ethoxyethoxy)ethanethiol
      C6 H14 O2 S
      LIAMZAFGRCLLJR-UHFFFAOYSA-N      		 Ligand Interaction
      MG
      Query on MG
      Download CCD File 
      A
      		MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.37 Å
      • R-Value Free: 0.266 
      • R-Value Work: 0.197 
      • R-Value Observed: 0.200 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 91.678α = 90
      b = 91.678β = 90
      c = 212.106γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      HKL-2000data scaling
      PDB_EXTRACTdata extraction
      PHASERphasing
      HKL-2000data collection
      HKL-2000data processing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      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