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 

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Ligand Structure Quality Assessment 


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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 DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack ...

    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)  |  3D 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)
UniProt & NIH Common Fund Data Resources
Find proteins for O15527 (Homo sapiens)
Explore O15527 
Go to UniProtKB:  O15527
PHAROS:  O15527
GTEx:  ENSG00000114026 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15527
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*AP*GP*GP*TP*C)-3')B 6Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*TP*GP*G)-3')C 5Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S5Y
Query on S5Y

Download Ideal Coordinates CCD File 
H [auth B]2-(2-ethoxyethoxy)ethanethiol
C6 H14 O2 S
LIAMZAFGRCLLJR-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth 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

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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