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- EMDB-19870: Human OGG1 bound to a nucleosome core particle with 8-oxodGuo les... -

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Basic information

Entry
Database: EMDB / ID: EMD-19870
TitleHuman OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0
Map data
Sample
  • Complex: Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle
    • Complex: Nucleosome core particle
      • Protein or peptide: N-glycosylase/DNA lyase
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H3.3
      • Protein or peptide: Histone H2A type 1-C
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • Complex: Widom 601 DNA
      • DNA: Widom 601 DNA (145-MER)
      • DNA: Widom 601 DNA (145-MER)
KeywordshOGG1 / 8-oxoguanine / nucleosome / base excision repair / DNA BINDING PROTEIN
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 / negative regulation of chromosome condensation / depyrimidination / Barr body ...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 / negative regulation of chromosome condensation / depyrimidination / Barr body / regulation of centromere complex assembly / 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 / pericentric heterochromatin formation / inner kinetochore / response to folic acid / muscle cell differentiation / oocyte maturation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / nucleosomal DNA binding / cellular response to cadmium ion / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / nucleus organization / spermatid development / response to light stimulus / single fertilization / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / nucleotide-excision repair / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cellular response to reactive oxygen species / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / response to radiation / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / base-excision repair / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / male gonad development / osteoblast differentiation / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization
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 / : ...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 / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
N-glycosylase/DNA lyase / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.3 / Histone H2A type 1-C
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRen M / Gut F / Fan Y / Hopfner K-P / Zhou C
Funding support China, Germany, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA0913800 China
National Natural Science Foundation of China (NSFC)22377059 China
German Research Foundation (DFG)SFB1361-project ID 393547839, TRR237-project ID 369799452, HO2489/11-1 Germany
German Research Foundation (DFG)Gottfried Wilhelm Leibniz-Price HO 2489/9-1 Germany
Chinese Scholarship Council China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles.
Authors: Mengtian Ren / Fabian Gut / Yilan Fan / Jingke Ma / Xiajing Shan / Aysenur Yikilmazsoy / Mariia Likhodeeva / Karl-Peter Hopfner / Chuanzheng Zhou /
Abstract: Base excision repair (BER) is initialized by DNA glycosylases, which recognize and flip damaged bases out of the DNA duplex into the enzymes active site, followed by cleavage of the glycosidic bond. ...Base excision repair (BER) is initialized by DNA glycosylases, which recognize and flip damaged bases out of the DNA duplex into the enzymes active site, followed by cleavage of the glycosidic bond. Recent studies have revealed that all types of DNA glycosylases repair base lesions less efficiently within nucleosomes, and their repair activity is highly depended on the lesion's location within the nucleosome. To reveal the underlying molecular mechanism of this phenomenon, we determine the 3.1 Å cryo-EM structure of human 8-oxoguanine-DNA glycosylase 1 (hOGG1) bound to a nucleosome core particle (NCP) containing a common oxidative base lesion, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo). Our structural analysis shows that hOGG1 can recognize and flip 8-oxodGuo even within NCPs; however, the interaction between 8-oxodGuo and hOGG1 in a NCP context is weaker than in free DNA due to competition for nucleosomal DNA by the histones. Binding of OGG1 and the flipping of 8-oxodGuo by hOGG1 leads to a partial detachment of DNA from the histone core and a ratchet-like inward movement of nucleosomal DNA. Our findings provide insights into how the dynamic structure of nucleosomes modulate the activity of repair enzymes within chromatin.
History
DepositionMar 16, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19870.png

Downloads & links

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Map

FileDownload / File: emd_19870.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 220 pix.
= 229.9 Å		1.05 Å/pix.
x 220 pix.
= 229.9 Å		1.05 Å/pix.
x 220 pix.
= 229.9 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.02280702 - 0.047702026
Average (Standard dev.)0.00025503218 (±0.0019307152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 229.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19870_msk_1.map
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Additional map: #1

Fileemd_19870_additional_1.map
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Half map: #2

Fileemd_19870_half_map_1.map
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Half map: #1

Fileemd_19870_half_map_2.map
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Sample components

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Entire : Binary complex of human 8-oxoguanine glycosylase with nucleosome ...

EntireName: Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle
Components
  • Complex: Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle
    • Complex: Nucleosome core particle
      • Protein or peptide: N-glycosylase/DNA lyase
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H3.3
      • Protein or peptide: Histone H2A type 1-C
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • Complex: Widom 601 DNA
      • DNA: Widom 601 DNA (145-MER)
      • DNA: Widom 601 DNA (145-MER)

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Supramolecule #1: Binary complex of human 8-oxoguanine glycosylase with nucleosome ...

SupramoleculeName: Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Widom 601 DNA

SupramoleculeName: Widom 601 DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: N-glycosylase/DNA lyase

MacromoleculeName: N-glycosylase/DNA lyase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.092289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSHHHHHHS QDPARALLPR RMGHRTLAST PALWASIPCP RSELRLDLVL PSGQSFRWRE QSPAHWSGVL ADQVWTLTQT EEQLHCTVY RGDKSQASRP TPDELEAVRK YFQLDVTLAQ LYHHWGSVDS HFQEVAQKFQ GVRLLRQDPI ECLFSFICSS N NNIARITG ...String:
GSSHHHHHHS QDPARALLPR RMGHRTLAST PALWASIPCP RSELRLDLVL PSGQSFRWRE QSPAHWSGVL ADQVWTLTQT EEQLHCTVY RGDKSQASRP TPDELEAVRK YFQLDVTLAQ LYHHWGSVDS HFQEVAQKFQ GVRLLRQDPI ECLFSFICSS N NNIARITG MVERLCQAFG PRLIQLDDVT YHGFPSLQAL AGPEVEAHLR KLGLGYRARY VSASARAILE EQGGLAWLQQ LR ESSYEEA HKALCILPGV GTQVADCICL MALDKPQAVP VDVHMWHIAQ RDYSWHPTTS QAKGPSPQTN KELGNFFRSL WGP YAGWAQ AVLFSADLRQ SRHAQEPPAK RRKGSKGPEG

UniProtKB: N-glycosylase/DNA lyase

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.229787 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP STGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.3

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Macromolecule #4: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.004329 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-C

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Macromolecule #5: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #6: Widom 601 DNA (145-MER)

MacromoleculeName: Widom 601 DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

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Macromolecule #7: Widom 601 DNA (145-MER)

MacromoleculeName: Widom 601 DNA (145-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.00766 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(8OG)(DA)(DT) (DT)(DC)(DT)(DG) (DA)(DT)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66370
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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