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- EMDB-15171: H1-free palindromic nucleosome, state D -

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Basic information

Entry
Database: EMDB / ID: EMD-15171
TitleH1-free palindromic nucleosome, state D
Map data
Sample
  • Complex: 197-bp H1-free palindromic nucleosome
    • Complex: Core histone octamer
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsAlegrio Louro J / Beinsteiner B / Cheng TC / Patel AKM / Boopathi R / Angelov D / Hamiche A / Bednar J / Kale S / Dimitrov S / Klaholz B
Funding support France, European Union, 7 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR) France
French Infrastructure for Integrated Structural Biology (FRISBI) France
Instruct-ERIC Center (Strasbourg Centre) France
Foundation for Medical Research (France) France
Institut National du Cancer (inCA) France
European Regional Development FundepiRNA - (Region Grand Est; Competitivite Alsace 2014-2020)European Union
CitationJournal: Structure / Year: 2023
Title: Nucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms.
Authors: Jaime Alegrio Louro / Ramachandran Boopathi / Brice Beinsteiner / Abdul Kareem Mohideen Patel / Tat Cheung Cheng / Dimitar Angelov / Ali Hamiche / Jan Bendar / Seyit Kale / Bruno P Klaholz / Stefan Dimitrov /
Abstract: Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome ...Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome structure, and therefore also to chromatin, is unclear. Efforts to investigate potential asymmetry due to H1s have been hampered by the DNA sequence, which naturally differs in each gyre. To overcome this issue, we designed and analyzed by cryo-EM a nucleosome reconstituted with a palindromic (601L) 197-bp DNA. As in the non-palindromic 601 sequence, H1 restricts linker DNA flexibility but reveals partial asymmetrical unwrapping. However, in contrast to the non-palindromic nucleosome, in the palindromic nucleosome H1 CTD collapses to the proximal linker. Molecular dynamics simulations show that this could be dictated by a slightly tilted orientation of the globular domain (GD) of H1, which could be linked to the DNA sequence of the nucleosome dyad.
History
DepositionJun 15, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15171.png

Downloads & links

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Map

FileDownload / File: emd_15171.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 232.1 Å		1.06 Å/pix.
x 220 pix.
= 232.1 Å		1.06 Å/pix.
x 220 pix.
= 232.1 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126
Minimum - Maximum-0.020245664 - 0.04512549
Average (Standard dev.)0.00031514987 (±0.0025211943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 232.09999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15171_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15171_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : 197-bp H1-free palindromic nucleosome

EntireName: 197-bp H1-free palindromic nucleosome
Components
  • Complex: 197-bp H1-free palindromic nucleosome
    • Complex: Core histone octamer

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Supramolecule #1: 197-bp H1-free palindromic nucleosome

SupramoleculeName: 197-bp H1-free palindromic nucleosome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#10
Details: 601L nucleosome with 25-bp sequence symmetric linkers
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: Core histone octamer

SupramoleculeName: Core histone octamer / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #4-#10
Source (natural)Organism: Homo sapiens (human)

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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: 7.6
Component:
ConcentrationFormulaName
5.0 mMNH2C(CH2OH)3HClTris-HCl
10.0 mMNaClSodium chloride
0.25 mMC10H16N2O8EDTA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Number grids imaged: 1 / #0 - Number real images: 3999 / #0 - Average exposure time: 10.0 sec. / #0 - Average electron dose: 49.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Number grids imaged: 1 / #1 - Number real images: 4891 / #1 - Average exposure time: 5.5 sec. / #1 - Average electron dose: 40.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nl0

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 17114
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.0)

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