2I5W

Structure of hOGG1 crosslinked to DNA sampling a normal G adjacent to an oxoG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex.

Banerjee, A., Verdine, G.L.

(2006) Proc.Natl.Acad.Sci.Usa 103: 15020-15025

  • DOI: 10.1073/pnas.0603644103

  • PubMed Abstract: 

    • How DNA glycosylases search through millions of base pairs and discriminate between rare sites of damage and otherwise undamaged bases is poorly understood. Even less understood are the details of the structural states arising from DNA glycosylases i ...

    How DNA glycosylases search through millions of base pairs and discriminate between rare sites of damage and otherwise undamaged bases is poorly understood. Even less understood are the details of the structural states arising from DNA glycosylases interacting with undamaged DNA. Recognizing the mutagenic lesion 7,8-dihydro-8-oxoguanine (8-oxoguanine, oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G), and buried in the structure of naked B-form DNA, oxoG and G are practically indistinguishable from each other. We have used disulfide cross-linking technology to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1) sampling an undamaged G:C base pair located adjacent to an oxoG:C base pair in DNA. The x-ray structure of the trapped complex reveals that the presence of the 8-oxoG drastically changes the local conformation of the extruded G. The extruded but intrahelical state of the G in this structure offers a view of an early intermediate in the base-extrusion pathway.

    Organizational Affiliation: 

    Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
N-glycosylase/DNA lyase
A
315Homo sapiensMutation(s): 1 
Gene Names: OGG1 (MMH, MUTM, OGH1)
Find proteins for O15527 (Homo sapiens)
Go to Gene View: OGG1
Go to UniProtKB:  O15527
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3'E12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*CP*AP*GP*(G42)P*TP*CP*TP*AP*C)-3'F10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
F
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.524α = 90.00
b = 91.524β = 90.00
c = 211.848γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
SCALEPACKdata scaling
HKL-2000data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description