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- EMDB-33177: Structure of nucleosome-DI complex (-55I, Apo state) -

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Basic information

Entry
Database: EMDB / ID: EMD-33177
TitleStructure of nucleosome-DI complex (-55I, Apo state)
Map data
Sample
  • Complex: complex
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (152-MER)
    • DNA: DNA (152-MER)
KeywordsNucleosome / AAG / Cryo-EM / DNA repair / Base excision repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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 / Histone H4, conserved site ...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 / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.8 Å
AuthorsZheng L / Tsai B / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Discov / Year: 2023
Title: Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome.
Authors: Lvqin Zheng / Bin Tsai / Ning Gao /
Abstract: The engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA ...The engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA glycosylases locate the substrate site on nucleosomes is currently unclear. Here, we report cryo-electron microscopy structures of nucleosomes bearing a deoxyinosine (DI) in various geometric positions and structures of them in complex with the DNA glycosylase AAG. The apo nucleosome structures show that the presence of a DI alone perturbs nucleosomal DNA globally, leading to a general weakening of the interface between DNA and the histone core and greater flexibility for the exit/entry of the nucleosomal DNA. AAG makes use of this nucleosomal plasticity and imposes further local deformation of the DNA through formation of the stable enzyme-substrate complex. Mechanistically, local distortion augmentation, translation/rotational register shift and partial opening of the nucleosome are employed by AAG to cope with substrate sites in fully exposed, occluded and completely buried positions, respectively. Our findings reveal the molecular basis for the DI-induced modification on the structural dynamics of the nucleosome and elucidate how the DNA glycosylase AAG accesses damaged sites on the nucleosome with different solution accessibility.
History
DepositionApr 1, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33177.png

Downloads & links

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Map

FileDownload / File: emd_33177.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 200 pix.
= 210.4 Å		1.05 Å/pix.
x 200 pix.
= 210.4 Å		1.05 Å/pix.
x 200 pix.
= 210.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0272
Minimum - Maximum-0.16848017 - 0.32285658
Average (Standard dev.)0.00044634298 (±0.008771687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 210.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33177_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33177_half_map_2.map
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

EntireName: complex
Components
  • Complex: complex
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (152-MER)
    • DNA: DNA (152-MER)

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Supramolecule #1: complex

SupramoleculeName: complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.421101 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.093436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: DNA (152-MER)

MacromoleculeName: DNA (152-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 47.170023 KDa
SequenceString: (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DI)(DC)(DA)(DC)(DG)(DT)(DG) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA) (DG)(DG)(DG)(DA)(DG)(DT) ...String:
(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DI)(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)(DG)(DA) (DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)

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Macromolecule #6: DNA (152-MER)

MacromoleculeName: DNA (152-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 46.655711 KDa
SequenceString: (DC)(DC)(DT)(DG)(DG)(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) ...String:
(DC)(DC)(DT)(DG)(DG)(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)(DC)(DC)(DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA) (DC)(DA)(DT) (DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 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:

7ohc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147071
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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