6W0M | pdb_00006w0m

Human 8-oxoguanine glycosylase crosslinked with oxoG lesion containing DNA

• PDB DOI: https://doi.org/10.2210/pdb6W0M/pdb
• NAKB: 6W0M

• Classification: Lyase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-03-02 Released: 2020-09-23 
• Deposition Author(s): Shigdel, U., Verdine, G.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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

• PubMed: 32895378 
• DOI: https://doi.org/10.1038/s41467-020-18290-2
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
LifeMine Therapeutics, 430 East 29th Street, Suite 830, New York, NY, 10016, USA.
Beam Therapeutics, 26 Landsdowne Street, 2nd Floor, Cambridge, MA, 02139, USA.
Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA.
Laboratoire de Chime Biophysique, Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 67000, Strasbourg, France.
Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, 76019-0065, USA. [e-mail].
Department of Chemistry, Umeå University, Umeå, SE 901 87, Sweden. [e-mail].
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. [e-mail].
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 44.36 kDa 
• Atom Count: 3,181 
• Modeled Residue Count: 342 
• Deposited Residue Count: 345 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A	317	Homo sapiens	Mutation(s): 3  Gene Names: OGG1, MMH, MUTM, OGH1 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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')	B	13	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')	C	15	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S5Y	F [auth A]	2-(2-ethoxyethoxy)ethanethiol C6 H14 O2 S LIAMZAFGRCLLJR-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.678	α = 90
b = 91.678	β = 90
c = 212.106	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data collection
HKL-2000	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Shigdel, U., Verdine, G.

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

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description