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- PDB-8j90: Cryo-EM structure of DDM1-nucleosome complex -

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Basic information

Entry
Database: PDB / ID: 8j90
TitleCryo-EM structure of DDM1-nucleosome complex
Components
  • (DNA (169-MER)) x 2
  • ATP-dependent DNA helicase DDM1
  • HTA6
  • HTB9
  • Histone H3.1
  • Histone H4
KeywordsNUCLEAR PROTEIN / Chromatin / Epigenetics / Histon variant / chromatin remodeler
Function / homology
Function and homology information


DNA-mediated transformation / retrotransposition / heterochromatin organization / chloroplast thylakoid / chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / plastid ...DNA-mediated transformation / retrotransposition / heterochromatin organization / chloroplast thylakoid / chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / plastid / chloroplast stroma / DNA methylation-dependent constitutive heterochromatin formation / pericentric heterochromatin / heterochromatin / DNA helicase activity / epigenetic regulation of gene expression / chloroplast / structural constituent of chromatin / peroxisome / nucleosome / heterochromatin formation / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / 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 / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H2B.6 / Histone H3.1 / Histone H4 / Probable histone H2A.7 / ATP-dependent DNA helicase DDM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.71 Å
AuthorsOsakabe, A. / Takizawa, Y. / Horikoshi, N. / Hatazawa, S. / Berger, F. / Kurumizaka, H. / Kakutani, T.
Funding support Japan, Austria, 13items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21K20628 Japan
Japan Society for the Promotion of Science (JSPS)JP22H05172 Japan
Japan Society for the Promotion of Science (JSPS)JP22H05178 Japan
Japan Science and TechnologyJPMJPR20K3 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Society for the Promotion of Science (JSPS)21H04977 Japan
Japan Society for the Promotion of Science (JSPS)23H00365 Japan
Austrian Science FundP33380 Austria
Austrian Science FundP32054 Austria
CitationJournal: Nat Commun / Year: 2024
Title: Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Authors: Akihisa Osakabe / Yoshimasa Takizawa / Naoki Horikoshi / Suguru Hatazawa / Lumi Negishi / Shoko Sato / Frédéric Berger / Tetsuji Kakutani / Hitoshi Kurumizaka /
Abstract: The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility ...The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.
History
DepositionMay 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
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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: HTA6
D: HTB9
E: Histone H3.1
F: Histone H4
G: HTA6
H: HTB9
I: DNA (169-MER)
J: DNA (169-MER)
K: ATP-dependent DNA helicase DDM1


Theoretical massNumber of molelcules
Total (without water)312,07411
Polymers312,07411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.1


Mass: 15583.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HTR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P59226
#2: Protein Histone H4


Mass: 11718.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P59259
#3: Protein HTA6 / HTA6


Mass: 16280.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FJE8
#4: Protein HTB9 / H2BAt / HTB9


Mass: 16756.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: H2B / Production host: Escherichia coli (E. coli) / References: UniProt: O23629
#7: Protein ATP-dependent DNA helicase DDM1 / AtDDM1


Mass: 87050.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DDM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XFH4, DNA helicase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (169-MER)


Mass: 51922.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Genus: Escherichia coli / Species: 562 / Description: plasmid DNA amplified by E.coli was used. / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (169-MER)


Mass: 52424.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Genus: Escherichia coli / Species: 562 / Description: plasmid DNA amplified by E.coli was used. / Production host: Escherichia coli (E. coli)

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Details

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 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
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: 25000 nm / Nominal defocus min: 10000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
9PHENIXmodel refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34559 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414635
ELECTRON MICROSCOPYf_angle_d0.75520688
ELECTRON MICROSCOPYf_dihedral_angle_d28.2383509
ELECTRON MICROSCOPYf_chiral_restr0.0422349
ELECTRON MICROSCOPYf_plane_restr0.0061844

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