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- EMDB-36085: Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W -

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Basic information

Entry
Database: EMDB / ID: EMD-36085
TitleCryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W
Map dataCryo-EM map of nucleosome containing Arabidopsis thaliana H2A.W
Sample
  • Complex: Nucleosome containing Arabidopsis thaliana H2A.W
    • Complex: Nucleosome
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: HTA6
      • Protein or peptide: HTB9
    • Complex: DNA
      • DNA: DNA (169-MER)
      • DNA: DNA (169-MER)
KeywordsChromatin / Epigenetics / Histon variant / chromatin remodeler / NUCLEAR PROTEIN
Function / homology
Function and homology information


chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / plastid / chloroplast stroma / heterochromatin / pericentric heterochromatin ...chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / plastid / chloroplast stroma / heterochromatin / pericentric heterochromatin / heterochromatin organization / chloroplast / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / protein heterodimerization activity / chromatin binding / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
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 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. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B.6 / Histone H3.1 / Histone H4 / Probable histone H2A.7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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: Takizawa Y / Horikoshi N / Hatazawa S / Negishi L / Sato S / Berger F / Kakutani T / Kurumizaka H / Osakabe A
History
DepositionMay 2, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36085.png

Downloads & links

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Map

FileDownload / File: emd_36085.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of nucleosome containing Arabidopsis thaliana H2A.W
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: 0.02
Minimum - Maximum-0.071850635 - 0.1320154
Average (Standard dev.)0.00025909592 (±0.0036704717)
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 nucleosome containing Arabidopsis thaliana H2A.W...

Fileemd_36085_additional_1.map
AnnotationCryo-EM map of nucleosome containing Arabidopsis thaliana H2A.W post-processed by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36085_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36085_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 : Nucleosome containing Arabidopsis thaliana H2A.W

EntireName: Nucleosome containing Arabidopsis thaliana H2A.W
Components
  • Complex: Nucleosome containing Arabidopsis thaliana H2A.W
    • Complex: Nucleosome
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: HTA6
      • Protein or peptide: HTB9
    • Complex: DNA
      • DNA: DNA (169-MER)
      • DNA: DNA (169-MER)

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Supramolecule #1: Nucleosome containing Arabidopsis thaliana H2A.W

SupramoleculeName: Nucleosome containing Arabidopsis thaliana H2A.W / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6

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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 #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
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: 59.1 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196430
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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