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- EMDB-36083: Cryo-EM structure of DDM1-nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36083
TitleCryo-EM structure of DDM1-nucleosome complex
Map dataCryo-EM map of DDM1-nucleosome complex
Sample
  • Complex: DDM1-nucleosome complex
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: HTA6
    • Protein or peptide: HTB9
    • DNA: DNA (169-MER)
    • DNA: DNA (169-MER)
    • Protein or peptide: ATP-dependent DNA helicase DDM1
KeywordsChromatin / Epigenetics / Histon variant / chromatin remodeler / NUCLEAR PROTEIN
Function / homology
Function and homology information


DNA-mediated transformation / retrotransposition / chloroplast thylakoid / heterochromatin organization / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / DNA methylation-dependent constitutive heterochromatin formation ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / heterochromatin organization / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / DNA methylation-dependent constitutive heterochromatin formation / ATP-dependent chromatin remodeler activity / plastid / chloroplast stroma / pericentric heterochromatin / heterochromatin / DNA helicase activity / epigenetic regulation of gene expression / chloroplast / heterochromatin formation / structural constituent of chromatin / nucleosome / peroxisome / 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 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 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)
Methodsingle 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, 13 items
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, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36083.png

Downloads & links

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Map

FileDownload / File: emd_36083.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of DDM1-nucleosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0115
Minimum - Maximum-0.017446795 - 0.037005566
Average (Standard dev.)0.00033551748 (±0.0019109768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM map of DDM1-nucleosome complex post-processed by DeepEMhancer

Fileemd_36083_additional_1.map
AnnotationCryo-EM map of DDM1-nucleosome complex post-processed by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36083_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36083_half_map_2.map
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

EntireName: DDM1-nucleosome complex
Components
  • Complex: DDM1-nucleosome complex
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: HTA6
    • Protein or peptide: HTB9
    • DNA: DNA (169-MER)
    • DNA: DNA (169-MER)
    • Protein or peptide: ATP-dependent DNA helicase DDM1

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Supramolecule #1: DDM1-nucleosome complex

SupramoleculeName: DDM1-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 300 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: 15.583246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRFRPGTV ALREIRKYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVAALQEA AEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

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: 11.718744 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKIFLENVI RDAVTYTEHA RRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: HTA6

MacromoleculeName: HTA6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.280221 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMESTGKV KKAFGGRKPP GAPKTKSVSK SMKAGLQFPV GRITRFLKKG RYAQRLGGGA PVYMAAVLEY LAAEVLELAG NAARDNKKS RIIPRHLLLA IRNDEELGKL LSGVTIAHGG VLPNINSVLL PKKSATKPAE EKATKSPVKS PKKA

UniProtKB: Probable histone H2A.7

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Macromolecule #4: HTB9

MacromoleculeName: HTB9 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.756738 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMAPRAEK KPAEKKPAAE KPVEEKSKAE KAPAEKKPKA GKKLPKEAGA GGDKKKKMKK KSVETYKIYI FKVLKQVHPD IGISSKAMG IMNSFINDIF EKLASESSKL ARYNKKPTIT SREIQTAVRL VLPGELAKHA VSEGTKAVTK FTSS

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: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 87.050062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPHMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ...String:
GPHMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ISRSKEDGET INSDLTEEET VIKLQNELCP LLTGGQLKSY QLKGVKWLIS LWQNGLNGIL ADQMGLGKTI QT IGFLSHL KGNGLDGPYL VIAPLSTLSN WFNEIARFTP SINAIIYHGD KNQRDELRRK HMPKTVGPKF PIVITSYEVA MND AKRILR HYPWKYVVID EGHRLKNHKC KLLRELKHLK MDNKLLLTGT PLQNNLSELW SLLNFILPDI FTSHDEFESW FDFS EKNKN EATKEEEEKR RAQVVSKLHG ILRPFILRRM KCDVELSLPR KKEIIMYATM TDHQKKFQEH LVNNTLEAHL GENAI RGQG WKGKLNNLVI QLRKNCNHPD LLQGQIDGSY LYPPVEEIVG QCGKFRLLER LLVRLFANNH KVLIFSQWTK LLDIMD YYF SEKGFEVCRI DGSVKLDERR RQIKDFSDEK SSCSIFLLST RAGGLGINLT AADTCILYDS DWNPQMDLQA MDRCHRI GQ TKPVHVYRLS TAQSIETRVL KRAYSKLKLE HVVIGQGQFH QERAKSSTPL EEEDILALLK EDETAEDKLI QTDISDAD L DRLLDRSDLT ITAPGETQAA EAFPVKGPGW EVVLPSSGGM LSSLNS

UniProtKB: ATP-dependent DNA helicase DDM1

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Macromolecule #5: DNA (169-MER)

MacromoleculeName: DNA (169-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.922059 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(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) (DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (169-MER)

MacromoleculeName: DNA (169-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.424352 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)(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)(DA)(DT)(DT) (DC)(DT)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG)(DC)(DT) (DC)(DG)(DC)(DG)(DA)(DT)(DA) (DG)(DG) (DG)(DT)(DC)(DC)(DG)(DA)(DT)

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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

BufferpH: 7.5
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 25.0 µm / Nominal defocus min: 10.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34559
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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