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- EMDB-37098: Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 -

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Basic information

Entry
Database: EMDB / ID: EMD-37098
TitleComplex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2
Map data
Sample
  • Complex: Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
    • Protein or peptide: Histone H2B.10
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.6
    • DNA: DNA (170-MER)
    • DNA: DNA (170-MER)
    • Protein or peptide: ATP-dependent DNA helicase DDM1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsDDM1 / nucleosome / H2A / STRUCTURAL PROTEIN
Function / homology
Function and homology information


DNA-mediated transformation / retrotransposition / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / DNA methylation-dependent constitutive heterochromatin formation / ATP-dependent chromatin remodeler activity / plastid ...DNA-mediated transformation / retrotransposition / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / DNA methylation-dependent constitutive heterochromatin formation / ATP-dependent chromatin remodeler activity / plastid / DNA helicase activity / epigenetic regulation of gene expression / chloroplast / response to bacterium / heterochromatin formation / response to wounding / structural constituent of chromatin / nucleosome / peroxisome / DNA helicase / chromatin remodeling / protein heterodimerization activity / nucleolus / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / 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. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3.1 / Histone H4 / Histone H2B.10 / Histone H2A.6 / ATP-dependent DNA helicase DDM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsZhang H / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2024
Title: Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures.
Authors: Hongwei Zhang / Zhanxi Gu / Yuan Zeng / Yu Zhang /
Abstract: The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we ...The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we determined the cryo-EM structures of DDM1-nucleosome and DDM1-nucleosome complexes at near-atomic resolution in the presence of the ATP analog ADP-BeFx. The structures show that nucleosomal DNA is unwrapped more on the surface of the histone octamer containing histone H2A than that containing histone H2A.W. DDM1 embraces one DNA gyre of the nucleosome and interacts with the N-terminal tails of histone H4. Although we did not observe DDM1-H2A.W interactions in our structures, the results of the pull-down experiments suggest a direct interaction between DDM1 and the core region of histone H2A.W. Our work provides mechanistic insights into the heterochromatin remodeling process driven by DDM1 in plants.
History
DepositionAug 7, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37098.png

Downloads & links

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Map

FileDownload / File: emd_37098.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.40091842 - 0.90111977
Average (Standard dev.)0.0040390813 (±0.035700466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37098_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37098_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2

EntireName: Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
Components
  • Complex: Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
    • Protein or peptide: Histone H2B.10
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.6
    • DNA: DNA (170-MER)
    • DNA: DNA (170-MER)
    • Protein or peptide: ATP-dependent DNA helicase DDM1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2

SupramoleculeName: Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Histone H2B.10

MacromoleculeName: Histone H2B.10 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.767544 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKADKKPAE KKPAEKTPAA EPAAAAEKKP KAGKKLPKEP AGAGDKKKKR SKKNVETYKI YIFKVLKQVH PDIGISSKAM GIMNSFIND IFEKLAGESS KLARYNKKPT ITSREIQTAV RLVLPGELAK HAVSEGTKAV TKFTSS

UniProtKB: Histone H2B.10

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Macromolecule #2: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.300968 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RFRPGTVALR EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VAALQEAAEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.436467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK IFLENVIRDA VTYTEHARRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A.6

MacromoleculeName: Histone H2A.6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.680854 KDa
Recombinant expressionOrganism: Escherichia coli 0.1197 (bacteria)
SequenceString:
MAGRGKTLGS GGAKKATSRS SKAGLQFPVG RIARFLKAGK YAERVGAGAP VYLAAVLEYL AAEVLELAGN AARDNKKTRI VPRHIQLAV RNDEELSKLL GDVTIANGGV MPNIHNLLLP KKAGASKPQE D

UniProtKB: Histone H2A.6

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Macromolecule #7: ATP-dependent DNA helicase DDM1

MacromoleculeName: ATP-dependent DNA helicase DDM1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 86.757758 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSLRSRKVI PASEMVSDGK TEKDASGDSP TSVLNEEENC EEKSVTVVEE EILLAKNGDS SLISEAMAQE EEQLLKLRED EEKANNAGS AVAPNLNETQ FTKLDELLTQ TQLYSEFLLE KMEDITINGI ESESQKAEPE KTGRGRKRKA ASQYNNTKAK R AVAAMISR ...String:
MVSLRSRKVI PASEMVSDGK TEKDASGDSP TSVLNEEENC EEKSVTVVEE EILLAKNGDS SLISEAMAQE EEQLLKLRED EEKANNAGS AVAPNLNETQ FTKLDELLTQ TQLYSEFLLE KMEDITINGI ESESQKAEPE KTGRGRKRKA ASQYNNTKAK R AVAAMISR SKEDGETINS DLTEEETVIK LQNELCPLLT GGQLKSYQLK GVKWLISLWQ NGLNGILADQ MGLGKTIQTI GF LSHLKGN GLDGPYLVIA PLSTLSNWFN EIARFTPSIN AIIYHGDKNQ RDELRRKHMP KTVGPKFPIV ITSYEVAMND AKR ILRHYP WKYVVIDEGH RLKNHKCKLL RELKHLKMDN KLLLTGTPLQ NNLSELWSLL NFILPDIFTS HDEFESWFDF SEKN KNEAT KEEEEKRRAQ VVSKLHGILR PFILRRMKCD VELSLPRKKE IIMYATMTDH QKKFQEHLVN NTLEAHLGEN AIRGQ GWKG KLNNLVIQLR KNCNHPDLLQ GQIDGSYLYP PVEEIVGQCG KFRLLERLLV RLFANNHKVL IFSQWTKLLD IMDYYF SEK GFEVCRIDGS VKLDERRRQI KDFSDEKSSC SIFLLSTRAG GLGINLTAAD TCILYDSDWN PQMDLQAMDR CHRIGQT KP VHVYRLSTAQ SIETRVLKRA YSKLKLEHVV IGQGQFHQER AKSSTPLEEE DILALLKEDE TAEDKLIQTD ISDADLDR L LDRSDLTITA PGETQAAEAF PVKGPGWEVV LPSSGGMLSS LNS

UniProtKB: ATP-dependent DNA helicase DDM1

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Macromolecule #5: DNA (170-MER)

MacromoleculeName: DNA (170-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.199215 KDa
SequenceString: (DA)(DT)(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) ...String:
(DA)(DT)(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)(DT)(DC)(DA) (DC)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DT)(DC)(DC) (DA)(DG)(DT)(DG)(DC)(DC)(DG) (DG)(DT) (DG)(DT)(DC)(DG)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (170-MER)

MacromoleculeName: DNA (170-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.764609 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DG)(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)(DG)(DA)(DT) (DT)(DC) (DT)(DC)(DC)(DA)(DG)(DG)(DA)(DT)

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Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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:

5x0y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239089
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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