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- PDB-8wh9: Structure of DDM1-nucleosome complex in ADP-BeFx state -

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Basic information

Entry
Database: PDB / ID: 8wh9
TitleStructure of DDM1-nucleosome complex in ADP-BeFx state
Components
  • ATP-dependent DNA helicase DDM1
  • DNA (antisense strand)
  • DNA (sense strand)
  • Histone H2A.6
  • Histone H2B.6
  • Histone H3.1
  • Histone H4
KeywordsGENE REGULATION / complex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex
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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsLiu, Y. / Zhang, Z. / Du, J.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A.6
D: Histone H2B.6
E: Histone H3.1
F: Histone H4
G: Histone H2A.6
H: Histone H2B.6
I: DNA (sense strand)
J: DNA (antisense strand)
K: ATP-dependent DNA helicase DDM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,87313
Polymers291,38011
Non-polymers4932
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.1


Mass: 15300.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: HTR2, At1g09200, T12M4.9, HTR3, At3g27360, K1G2.8, HTR13, At5g10390, F12B17_260, HTR9, At5g10400, F12B17_250, HTR1, At5g65360, MNA5.9
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P59226
#2: Protein Histone H4


Mass: 11436.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: At1g07660, F24B9.25, At1g07820, F24B9.8, At2g28740, F8N16.2, T11P11.4, At3g45930, F16L2_140, At3g46320, F18L15.40, At3g53730, F5K20_30, At5g59690, MTH12.10, At5g59970, MMN10.22
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P59259
#3: Protein Histone H2A.6 / HTA1 / Protein RESISTANT TO AGROBACTERIUM TRANSFORMATION 5


Mass: 13680.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAT5, H2A-1, At5g54640, MRB17.14 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9LD28
#4: Protein Histone H2B.6 / H2BAt / HTB9


Mass: 16474.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: H2B, At3g45980, F16L2.190 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O23629
#7: Protein ATP-dependent DNA helicase DDM1 / Protein CHROMATIN REMODELING 1 / AtCHR1 / CHR01 / Protein DECREASED DNA METHYLATION 1 / AtDDM1 / ...Protein CHROMATIN REMODELING 1 / AtCHR1 / CHR01 / Protein DECREASED DNA METHYLATION 1 / AtDDM1 / Protein SOMNIFEROUS 1 / SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin DDM1


Mass: 86844.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DDM1, CHA1, CHR1, SOM1, SOM4, At5g66750, MSN2.14 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9XFH4, DNA helicase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (sense strand)


Mass: 45123.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (antisense strand)


Mass: 45626.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DDM1-nucleosome complex in ADP-BeFx state / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.29 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6776
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3898721
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156597 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0116209
ELECTRON MICROSCOPYf_angle_d1.44323103
ELECTRON MICROSCOPYf_dihedral_angle_d25.3636541
ELECTRON MICROSCOPYf_chiral_restr0.1222618
ELECTRON MICROSCOPYf_plane_restr0.0071930

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