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- EMDB-28448: Cryo-ET 3D reconstruction of an individual tetra-nucleosome parti... -

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Basic information

Entry
Database: EMDB / ID: EMD-28448
TitleCryo-ET 3D reconstruction of an individual tetra-nucleosome particle in 50 mM NaCl and 20 mM HEPES buffer --- Particle #157
Map dataCryo-ET 3D reconstruction of an individual tetra-nucleosome particle in 50 mM NaCl and 20 mM HEPES buffer --- Particle #157
Sample
  • Complex: Tetranucleosome array
KeywordsNucleosome Array / DNA BINDING PROTEIN
Biological speciesXenopus (frog)
Methodelectron tomography / cryo EM
AuthorsZhang M / Celis CD / Liu JF / Bustamante C / Ren G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) United States
CitationJournal: To Be Published
Title: Individual-molecule 3D structures reveal nucleosome array dynamics and regulations
Authors: Zhang M / Celis CD / Liu JF / Bustamante C / Ren G
History
DepositionOct 4, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28448.png

Downloads & links

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Map

FileDownload / File: emd_28448.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET 3D reconstruction of an individual tetra-nucleosome particle in 50 mM NaCl and 20 mM HEPES buffer --- Particle #157
Voxel sizeX=Y=Z: 7.4 Å
Density
Minimum - Maximum-0.2628925 - 0.9682609
Average (Standard dev.)0.000606899 (±0.014082463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 1480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tetranucleosome array

EntireName: Tetranucleosome array
Components
  • Complex: Tetranucleosome array

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Supramolecule #1: Tetranucleosome array

SupramoleculeName: Tetranucleosome array / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus (frog)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 50 mM NaCl 20 mM HEPES 1 mM DTT 1 mM EDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 5.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: SPIDER / Number images used: 35

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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