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- PDB-8kcb: Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 -

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Basic information

Entry
Database: PDB / ID: 8kcb
TitleComplex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2
Components
  • (DNA (170-MER)) x 2
  • ATP-dependent DNA helicase DDM1
  • Histone H2A.6
  • Histone H2B.10
  • Histone H3.1
  • Histone H4
KeywordsSTRUCTURAL PROTEIN / DDM1 / nucleosome / H2A
Function / homology
Function and homology information


DNA-mediated transformation / retrotransposition / chromocenter / thylakoid / response to water deprivation / plant-type vacuole / plasmodesma / plastid / DNA methylation-dependent constitutive heterochromatin formation / DNA helicase activity ...DNA-mediated transformation / retrotransposition / chromocenter / thylakoid / response to water deprivation / plant-type vacuole / plasmodesma / 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 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsZhang, H. / Zhang, Y.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Histone H2B.10
C: Histone H2B.10
F: Histone H3.1
E: Histone H3.1
H: Histone H4
G: Histone H4
A: Histone H2A.6
B: Histone H2A.6
I: DNA (170-MER)
J: DNA (170-MER)
K: ATP-dependent DNA helicase DDM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,58613
Polymers304,09311
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 DCFEHGABK

#1: Protein Histone H2B.10 / HTB2


Mass: 15767.544 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g22880, MRN17.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FFC0
#2: 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 (E. coli) / References: UniProt: P59226
#3: 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 (E. coli) / References: UniProt: P59259
#4: 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 0.1197 (bacteria) / References: UniProt: Q9LD28
#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: 86757.758 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9XFH4, DNA helicase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (170-MER)


Mass: 52199.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (170-MER)


Mass: 52764.609 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 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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: Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239089 / Symmetry type: POINT
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214738
ELECTRON MICROSCOPYf_angle_d0.45221026
ELECTRON MICROSCOPYf_dihedral_angle_d23.5357962
ELECTRON MICROSCOPYf_chiral_restr0.032450
ELECTRON MICROSCOPYf_plane_restr0.0031794

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