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- EMDB-43607: Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle -

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Basic information

Entry
Database: EMDB / ID: EMD-43607
TitleHuman OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle
Map dataHuman OGG1 binding at 8-oxoG on a 35 bp DNA half map 1
Sample
  • Complex: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
    • DNA: DNA (35-MER)
    • DNA: DNA (35-MER)
    • Protein or peptide: N-glycosylase/DNA lyase
KeywordsHuman OGG1 binding at 8-oxoG of a 35 bp DNA duplex / HYDROLASE / LYASE-DNA complex
Function / homology
Function and homology information


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYou Q / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ES011858 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM131754 United States
CitationJournal: Commun Biol / Year: 2024
Title: Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations.
Authors: Qinglong You / Xiang Feng / Yi Cai / Stephen B Baylin / Huilin Li /
Abstract: The human glycosylase OGG1 extrudes and excises the oxidized DNA base 8-oxoguanine (8-oxoG) to initiate base excision repair and plays important roles in many pathological conditions such as cancer, ...The human glycosylase OGG1 extrudes and excises the oxidized DNA base 8-oxoguanine (8-oxoG) to initiate base excision repair and plays important roles in many pathological conditions such as cancer, inflammation, and neurodegenerative diseases. Previous structural studies have used a truncated protein and short linear DNA, so it has been unclear how full-length OGG1 operates on longer DNA or on nucleosomes. Here we report cryo-EM structures of human OGG1 bound to a 35-bp long DNA containing an 8-oxoG within an unmethylated Cp-8-oxoG dinucleotide as well as to a nucleosome with an 8-oxoG at super-helical location (SHL)-5. The 8-oxoG in the linear DNA is flipped out by OGG1, consistent with previous crystallographic findings with a 15-bp DNA. OGG1 preferentially binds near dsDNA ends at the nucleosomal entry/exit sites. Such preference may underlie the enzyme's function in DNA double-strand break repair. Unexpectedly, we find that OGG1 bends the nucleosomal entry DNA, flips an undamaged guanine, and binds to internal nucleosomal DNA sites such as SHL-5 and SHL+6. We suggest that the DNA base search mechanism by OGG1 may be chromatin context-dependent and that OGG1 may partner with chromatin remodelers to excise 8-oxoG at the nucleosomal internal sites.
History
DepositionFeb 3, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43607.png

Downloads & links

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Map

FileDownload / File: emd_43607.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman OGG1 binding at 8-oxoG on a 35 bp DNA half map 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 200 pix.
= 165.6 Å		0.83 Å/pix.
x 200 pix.
= 165.6 Å		0.83 Å/pix.
x 200 pix.
= 165.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00758
Minimum - Maximum-0.06402119 - 0.08919578
Average (Standard dev.)0.00019045289 (±0.0023196598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 165.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human OGG1 binding at 8-oxoG on a 35 bp DNA

Fileemd_43607_half_map_1.map
AnnotationHuman OGG1 binding at 8-oxoG on a 35 bp DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human OGG1 binding at 8-oxoG on a 35 bp DNA half map 2

Fileemd_43607_half_map_2.map
AnnotationHuman OGG1 binding at 8-oxoG on a 35 bp DNA half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG

EntireName: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
Components
  • Complex: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
    • DNA: DNA (35-MER)
    • DNA: DNA (35-MER)
    • Protein or peptide: N-glycosylase/DNA lyase

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Supramolecule #1: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG

SupramoleculeName: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.695851 KDa
SequenceString:
(DA)(DT)(DG)(DC)(DC)(DT)(DC)(DG)(DC)(DA) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(8OG)(DC) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)

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Macromolecule #2: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.861943 KDa
SequenceString:
(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC)(DA)(DG)(DC)(DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DG)(DC)(DG) (DA)(DG)(DG)(DC)(DA)(DT)

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Macromolecule #3: N-glycosylase/DNA lyase

MacromoleculeName: N-glycosylase/DNA lyase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.72002 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGHHHHHHDY KDHDGDYKDH DIDYKDDDDK ENLYFQGGGG GSDPARALLP RRMGHRTLAS TPALWASIPC PRSELRLDLV LPSGQSFRW REQSPAHWSG VLADQVWTLT QTEEQLHCTV YRGDKSQASR PTPDELEAVR KYFQLDVTLA QLYHHWGSVD S HFQEVAQK ...String:
MGHHHHHHDY KDHDGDYKDH DIDYKDDDDK ENLYFQGGGG GSDPARALLP RRMGHRTLAS TPALWASIPC PRSELRLDLV LPSGQSFRW REQSPAHWSG VLADQVWTLT QTEEQLHCTV YRGDKSQASR PTPDELEAVR KYFQLDVTLA QLYHHWGSVD S HFQEVAQK FQGVRLLRQD PIECLFSFIC SSNNNIARIT GMVERLCQAF GPRLIQLDDV TYHGFPSLQA LAGPEVEAHL RK LGLGYRA RYVSASARAI LEEQGGLAWL QQLRESSYEE AHKALCILPG VGTQVADCIC LMALDKPQAV PVDVHMWHIA QRD YSWHPT TSQAKGPSPQ TNKELGNFFR SLWGPYAGWA QAVLFSADLR QSRHAQEPPA KRRKGSKGPE G

UniProtKB: N-glycosylase/DNA lyase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1ebm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2144984
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8vx4:
Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle

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