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- PDB-23tv: Cryo-EM structure of Arabidopsis H3-H4 octasome class3 -

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Basic information

Entry
Database: PDB / ID: 23tv
TitleCryo-EM structure of Arabidopsis H3-H4 octasome class3
Components
  • (DNA (Widom 601)) x 2
  • Histone H3.1
  • Histone H4
KeywordsNUCLEAR PROTEIN / H3-H4 octasome / chromatin / histone / nucleosome-like structure / nucleosome / Arabidopsis H3-H4 octasome
Function / homology
Function and homology information


chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / plastid / chloroplast / nucleosomal DNA binding / structural constituent of chromatin / nucleosome ...chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / plastid / chloroplast / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / peroxisome / heterochromatin formation / protein heterodimerization activity / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
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 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 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3.1 / Histone H4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsHaga, J. / Takasuka, T.E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other privateG-2025-2-039 Japan
CitationJournal: To Be Published
Title: Structures of the Arabidopsis nucleosome and H3-H4 octasome assembled in a wheat germ cell-free co-expression chromatin assembly platform
Authors: Haga, J. / Banko, P. / Okimune, K. / Azuma, T. / Terashi, G. / Morishita, R. / Kita, S. / Maenaka, K. / Kihara, D. / Takasuka, T.E.
History
DepositionFeb 16, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H3.1
D: Histone H4
E: Histone H3.1
F: Histone H4
G: Histone H3.1
H: Histone H4
I: DNA (Widom 601)
J: DNA (Widom 601)


Theoretical massNumber of molelcules
Total (without water)451,67110
Polymers451,67110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Histone H3.1


Mass: 15300.968 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0
Gene: HTR2, At1g09200, T12M4.9, HTR3, At3g27360, K1G2.8, HTR13, At5g10390, F12B17_260, HTR9, At5g10400, F12B17_250, HTR1, At5g65360, MNA5.9
Plasmid: pEU vector / Production host: Triticum aestivum (bread wheat) / References: UniProt: P59226
#2: Protein
Histone H4


Mass: 11436.467 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0
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
Plasmid: pEU vector / Production host: Triticum aestivum (bread wheat) / References: UniProt: P59259
#3: DNA chain DNA (Widom 601)


Mass: 171477.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (Widom 601)


Mass: 173243.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: Arabidopsis thaliana H3-H4 octasome reconstituted on Widom 601 DNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Col-0
Source (recombinant)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
21 mMDTTC4H10O2S21
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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.1particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARCv4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70192 / Symmetry type: POINT
RefinementHighest resolution: 3.49 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310414
ELECTRON MICROSCOPYf_angle_d0.5315086
ELECTRON MICROSCOPYf_dihedral_angle_d30.9083293
ELECTRON MICROSCOPYf_chiral_restr0.031723
ELECTRON MICROSCOPYf_plane_restr0.0031076

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