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- EMDB-43611: Human OGG1 bound at the nucleosomal super helical location +6 -

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Basic information

Entry
Database: EMDB / ID: EMD-43611
TitleHuman OGG1 bound at the nucleosomal super helical location +6
Map dataHuman OGG1 binds nucleosome at SHL 6
Sample
  • Complex: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
KeywordsNucleosome core particle containing 8-oxoG DNA damage / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 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_43611.png

Downloads & links

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Map

FileDownload / File: emd_43611.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman OGG1 binds nucleosome at SHL 6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 160 pix.
= 264.96 Å		1.66 Å/pix.
x 160 pix.
= 264.96 Å		1.66 Å/pix.
x 160 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.023608128 - 0.07463651
Average (Standard dev.)0.0000050008143 (±0.003790131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human OGG1 binds nucleosome at SHL 6 half map 1

Fileemd_43611_half_map_1.map
AnnotationHuman OGG1 binds nucleosome at SHL 6 half map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Human OGG1 binds nucleosome at SHL 6 half map 2

Fileemd_43611_half_map_2.map
AnnotationHuman OGG1 binds nucleosome at SHL 6 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

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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
Source (natural)Organism: Homo sapiens (human)

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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:

6fq5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155394
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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