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- EMDB-37537: Structure of DDM1-nucleosome complex in the ADP-BeFx state with D... -

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Basic information

Entry
Database: EMDB / ID: EMD-37537
TitleStructure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Map dataDDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Sample
  • Complex: DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.6
    • Protein or peptide: Histone H2B.6
    • DNA: DNA (sense strand)
    • DNA: DNA (antisense strand)
    • Protein or peptide: ATP-dependent DNA helicase DDM1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordscomplex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex / GENE REGULATION
Function / homology
Function and homology information


DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / thylakoid / response to water deprivation / plant-type vacuole / plasmodesma / chloroplast stroma / plastid ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / thylakoid / response to water deprivation / plant-type vacuole / plasmodesma / chloroplast stroma / plastid / DNA methylation-dependent constitutive heterochromatin formation / DNA helicase activity / epigenetic regulation of gene expression / chloroplast / response to bacterium / response to wounding / structural constituent of chromatin / peroxisome / nucleosome / heterochromatin formation / 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 H2A conserved site / Histone H2A signature. / Histone H2B ...HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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 H2B.6 / Histone H3.1 / Histone H4 / 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: 4.05 Å
AuthorsLiu Y / Zhang Z / Du J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2024
Title: Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
Authors: Yue Liu / Zhihui Zhang / Hongmiao Hu / Wei Chen / Fan Zhang / Qian Wang / Changshi Wang / Kaige Yan / Jiamu Du /
Abstract: Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers. In plants, ...Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeF-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeF-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.
History
DepositionSep 22, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37537.png

Downloads & links

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Map

FileDownload / File: emd_37537.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.024935551 - 0.052177858
Average (Standard dev.)0.000388745 (±0.0023694013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half1 map of DDM1-nucleosome complex in the ADP-BeFx...

Fileemd_37537_half_map_1.map
AnnotationHalf1 map of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2 map of DDM1-nucleosome complex in the ADP-BeFx...

Fileemd_37537_half_map_2.map
AnnotationHalf2 map of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to ...

EntireName: DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Components
  • Complex: DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.6
    • Protein or peptide: Histone H2B.6
    • DNA: DNA (sense strand)
    • DNA: DNA (antisense strand)
    • Protein or peptide: ATP-dependent DNA helicase DDM1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to ...

SupramoleculeName: DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 376 KDa

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / 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 #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / 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 #3: Histone H2A.6

MacromoleculeName: Histone H2A.6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.680854 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGRGKTLGS GGAKKATSRS SKAGLQFPVG RIARFLKAGK YAERVGAGAP VYLAAVLEYL AAEVLELAGN AARDNKKTRI VPRHIQLAV RNDEELSKLL GDVTIANGGV MPNIHNLLLP KKAGASKPQE D

UniProtKB: Histone H2A.6

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Macromolecule #4: Histone H2B.6

MacromoleculeName: Histone H2B.6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.474459 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAPRAEKKPA EKKPAAEKPV EEKSKAEKAP AEKKPKAGKK LPKEAGAGGD KKKKMKKKSV ETYKIYIFKV LKQVHPDIGI SSKAMGIMN SFINDIFEKL ASESSKLARY NKKPTITSRE IQTAVRLVLP GELAKHAVSE GTKAVTKFTS S

UniProtKB: Histone H2B.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: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 86.844836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMVSLRSRKV IPASEMVSDG KTEKDASGDS PTSVLNEEEN CEEKSVTVVE EEILLAKNGD SSLISEAMAQ EEEQLLKLRE DEEKANNAG SAVAPNLNET QFTKLDELLT QTQLYSEFLL EKMEDITING IESESQKAEP EKTGRGRKRK AASQYNNTKA K RAVAAMIS ...String:
SMVSLRSRKV IPASEMVSDG KTEKDASGDS PTSVLNEEEN CEEKSVTVVE EEILLAKNGD SSLISEAMAQ EEEQLLKLRE DEEKANNAG SAVAPNLNET QFTKLDELLT QTQLYSEFLL EKMEDITING IESESQKAEP EKTGRGRKRK AASQYNNTKA K RAVAAMIS RSKEDGETIN SDLTEEETVI KLQNELCPLL TGGQLKSYQL KGVKWLISLW QNGLNGILAD QMGLGKTIQT IG FLSHLKG NGLDGPYLVI APLSTLSNWF NEIARFTPSI NAIIYHGDKN QRDELRRKHM PKTVGPKFPI VITSYEVAMN DAK RILRHY PWKYVVIDEG HRLKNHKCKL LRELKHLKMD NKLLLTGTPL QNNLSELWSL LNFILPDIFT SHDEFESWFD FSEK NKNEA TKEEEEKRRA QVVSKLHGIL RPFILRRMKC DVELSLPRKK EIIMYATMTD HQKKFQEHLV NNTLEAHLGE NAIRG QGWK GKLNNLVIQL RKNCNHPDLL QGQIDGSYLY PPVEEIVGQC GKFRLLERLL VRLFANNHKV LIFSQWTKLL DIMDYY FSE KGFEVCRIDG SVKLDERRRQ IKDFSDEKSS CSIFLLSTRA GGLGINLTAA DTCILYDSDW NPQMDLQAMD RCHRIGQ TK PVHVYRLSTA QSIETRVLKR AYSKLKLEHV VIGQGQFHQE RAKSSTPLEE EDILALLKED ETAEDKLIQT DISDADLD R LLDRSDLTIT APGETQAAEA FPVKGPGWEV VLPSSGGMLS SLNS

UniProtKB: ATP-dependent DNA helicase DDM1

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Macromolecule #5: DNA (sense strand)

MacromoleculeName: DNA (sense strand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.123758 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(DA)(DA)(DC)(DC)(DG)(DC)(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) (DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (antisense strand)

MacromoleculeName: DNA (antisense strand) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.626043 KDa
SequenceString: (DA)(DT)(DC)(DG)(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) ...String:
(DA)(DT)(DC)(DG)(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)(DG)(DC)(DG)(DG)(DT) (DT)(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)(DG)(DA)(DT)

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Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 2 / 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: 2 / 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

Concentration2.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 6776 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3898721
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 24191
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8wha:
Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2

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