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- EMDB-15232: H1-bound palindromic nucleosome, state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-15232
TitleH1-bound palindromic nucleosome, state 1
Map data
Sample
  • Complex: 197-bp H1-bound palindromic nucleosome
    • Complex: Histone H1.0-B
    • Complex: Core histone octamer
Function / homology
Function and homology information


negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H1.0-B / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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 23, 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_15232.png

Downloads & links

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Map

FileDownload / File: emd_15232.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00742
Minimum - Maximum-0.020836687 - 0.04135812
Average (Standard dev.)0.00029250135 (±0.0021857093)
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_15232_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_15232_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 197-bp H1-bound palindromic nucleosome

EntireName: 197-bp H1-bound palindromic nucleosome
Components
  • Complex: 197-bp H1-bound palindromic nucleosome
    • Complex: Histone H1.0-B
    • Complex: Core histone octamer

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

SupramoleculeName: 197-bp H1-bound palindromic nucleosome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#10
Details: 601L nucleosome with 25-bp sequence symmetric linkers and bound to linker histone H1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Supramolecule #2: Histone H1.0-B

SupramoleculeName: Histone H1.0-B / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: Core histone octamer

SupramoleculeName: Core histone octamer / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #4-#10

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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: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 6284
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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Atomic model buiding 1

Initial modelPDB ID:

5nl0

RefinementSpace: REAL
Output model

PDB-8aag:
H1-bound palindromic nucleosome, state 1

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