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- EMDB-43610: Human OGG1 bound at the nucleosomal super helical location -5 -

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Basic information

Entry
Database: EMDB / ID: EMD-43610
TitleHuman OGG1 bound at the nucleosomal super helical location -5
Map dataHuman OGG1 binds nucleosome at SHL -5
Sample
  • Complex: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
    • Protein or peptide: OGG1
KeywordsNucleosome core particle containing 8-oxoG DNA damage / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 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_43610.png

Downloads & links

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Map

FileDownload / File: emd_43610.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman OGG1 binds nucleosome at SHL -5
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-0.018758833 - 0.0671569
Average (Standard dev.)-0.000092200265 (±0.0037376347)
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 -5 half map 1

Fileemd_43610_half_map_1.map
AnnotationHuman OGG1 binds nucleosome at SHL -5 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 -5 half map 2

Fileemd_43610_half_map_2.map
AnnotationHuman OGG1 binds nucleosome at SHL -5 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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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
    • Protein or peptide: OGG1

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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: OGG1

MacromoleculeName: OGG1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHDY KDHDGDYKDH DIDYKDDDDK ENLYFQGGGG GSDPARALLP RRMGHRTLAS TPALWASIPC PRSELRLDLV LPSGQSFRWR EQSPAHWSGV LADQVWTLTQ TEEQLHCTVY RGDKSQASRP TPDELEAVRK YFQLDVTLAQ LYHHWGSVDS HFQEVAQKFQ ...String:
MGHHHHHHDY KDHDGDYKDH DIDYKDDDDK ENLYFQGGGG GSDPARALLP RRMGHRTLAS TPALWASIPC PRSELRLDLV LPSGQSFRWR EQSPAHWSGV LADQVWTLTQ TEEQLHCTVY RGDKSQASRP TPDELEAVRK YFQLDVTLAQ LYHHWGSVDS HFQEVAQKFQ GVRLLRQDPI ECLFSFICSS NNNIARITGM VERLCQAFGP RLIQLDDVTY HGFPSLQALA GPEVEAHLRK LGLGYRARYV SASARAILEE QGGLAWLQQL RESSYEEAHK ALCILPGVGT QVADCICLMA LDKPQAVPVD VHMWHIAQRD YSWHPTTSQA KGPSPQTNKE LGNFFRSLWG PYAGWAQAVL FSADLRQSRH AQEPPAKRRK GSKGPEG

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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: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51710
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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