+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43611 | |||||||||
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Title | Human OGG1 bound at the nucleosomal super helical location +6 | |||||||||
Map data | Human OGG1 binds nucleosome at SHL 6 | |||||||||
Sample |
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Keywords | Nucleosome core particle containing 8-oxoG DNA damage / DNA BINDING PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | You Q / Li H | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43611.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-43611-v30.xml emd-43611.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_43611.png | 57.6 KB | ||
Filedesc metadata | emd-43611.cif.gz | 3.9 KB | ||
Others | emd_43611_half_map_1.map.gz emd_43611_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43611 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43611 | HTTPS FTP |
-Validation report
Summary document | emd_43611_validation.pdf.gz | 734.5 KB | Display | EMDB validaton report |
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Full document | emd_43611_full_validation.pdf.gz | 734.1 KB | Display | |
Data in XML | emd_43611_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_43611_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43611 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43611 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43611.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human OGG1 binds nucleosome at SHL 6 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.656 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Human OGG1 binds nucleosome at SHL 6 half map 1
File | emd_43611_half_map_1.map | ||||||||||||
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Annotation | Human OGG1 binds nucleosome at SHL 6 half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human OGG1 binds nucleosome at SHL 6 half map 2
File | emd_43611_half_map_2.map | ||||||||||||
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Annotation | Human OGG1 binds nucleosome at SHL 6 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
Entire | Name: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG |
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Components |
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-Supramolecule #1: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG
Supramolecule | Name: Complex of Human OGG1 with a 35 bp DNA duplex containing 8-oxoG type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155394 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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