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- EMDB-19134: Cryo-EM structure of nucleosome containing Widom603 DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-19134
TitleCryo-EM structure of nucleosome containing Widom603 DNA
Map data
Sample
  • Complex: Human nucleosome containing Widom 603 DNA sequence
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: Widom 603 DNA sequence
    • DNA: Widom 603 DNA sequence
Keywordsnucleosome / histone complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / 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 / Deposition of new CENPA-containing nucleosomes at the centromere ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / epigenetic regulation of gene expression / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / killing of cells of another organism / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 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
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMotorin NA / Afonin D / Armeev GA / Moiseenko A / Zhao L / Vasiliev V / Oleinikov P / Shaytan A / Shi X / Studitsky V / Sokolova O
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-30003 Russian Federation
CitationJournal: Structure / Year: 2025
Title: Structure and dynamics of a nucleosome core particle based on Widom 603 DNA sequence.
Authors: Grigoriy A Armeev / Andrey V Moiseenko / Nikita A Motorin / Dmitriy A Afonin / Lei Zhao / Veniamin A Vasilev / Pavel D Oleinikov / Grigory S Glukhov / Georgy S Peters / Vasily M Studitsky / ...Authors: Grigoriy A Armeev / Andrey V Moiseenko / Nikita A Motorin / Dmitriy A Afonin / Lei Zhao / Veniamin A Vasilev / Pavel D Oleinikov / Grigory S Glukhov / Georgy S Peters / Vasily M Studitsky / Alexey V Feofanov / Alexey K Shaytan / Xiangyan Shi / Olga S Sokolova /
Abstract: Nucleosomes are fundamental elements of chromatin organization that participate in compacting genomic DNA and serve as targets for the binding of numerous regulatory proteins. Currently, over 500 ...Nucleosomes are fundamental elements of chromatin organization that participate in compacting genomic DNA and serve as targets for the binding of numerous regulatory proteins. Currently, over 500 different nucleosome structures are known. Despite the large number of nucleosome structures, all of them were formed on only about twenty different DNA sequences. Using cryo-electron microscopy, we determined the structure of the nucleosome formed on a high-affinity Widom 603 DNA sequence at 4 Å resolution; an atomic model was built. We proposed an integrative modeling approach to study the nucleosomal DNA unwrapping based on the cryoelectron microscopy (cryo-EM) data. We also demonstrated the DNA unwrapping of the Widom 603 nucleosome using small angle X-ray scattering and single particle Förster resonance energy transfer measurements. Our results are consistent with the asymmetry of nucleosomal DNA unwrapping. Our data revealed the dependence of nucleosome structure and dynamics on the sequence of nucleosomal DNA.
History
DepositionDec 14, 2023-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19134.png

Downloads & links

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Map

FileDownload / File: emd_19134.map.gz / Format: CCP4 / Size: 6.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 84 pix.
= 69.72 Å		0.83 Å/pix.
x 144 pix.
= 119.52 Å		0.83 Å/pix.
x 135 pix.
= 112.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.36586747 - 0.52866614
Average (Standard dev.)0.023833612 (±0.06258501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin147156183
Dimensions14413584
Spacing84144135
CellA: 69.72 Å / B: 119.520004 Å / C: 112.05 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19134_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_19134_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 : Human nucleosome containing Widom 603 DNA sequence

EntireName: Human nucleosome containing Widom 603 DNA sequence
Components
  • Complex: Human nucleosome containing Widom 603 DNA sequence
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: Widom 603 DNA sequence
    • DNA: Widom 603 DNA sequence

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Supramolecule #1: Human nucleosome containing Widom 603 DNA sequence

SupramoleculeName: Human nucleosome containing Widom 603 DNA sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 15.305969 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.804045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #5: Widom 603 DNA sequence

MacromoleculeName: Widom 603 DNA sequence / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.608406 KDa
SequenceString: (DC)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DC)(DG) (DC)(DG)(DC)(DC)(DC)(DA)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DT)(DG)(DT)(DG)(DA)(DA) (DG)(DT)(DC)(DG)(DT)(DC)(DA)(DC)(DT)(DC) (DG) (DG)(DG)(DC)(DT)(DT)(DC) ...String:
(DC)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DC)(DG) (DC)(DG)(DC)(DC)(DC)(DA)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DT)(DG)(DT)(DG)(DA)(DA) (DG)(DT)(DC)(DG)(DT)(DC)(DA)(DC)(DT)(DC) (DG) (DG)(DG)(DC)(DT)(DT)(DC)(DT)(DA) (DA)(DG)(DT)(DA)(DC)(DG)(DC)(DT)(DT)(DA) (DG)(DG) (DC)(DC)(DA)(DC)(DG)(DG)(DT) (DA)(DG)(DA)(DG)(DG)(DG)(DC)(DA)(DA)(DT) (DC)(DC)(DA) (DA)(DG)(DG)(DC)(DT)(DA) (DA)(DC)(DC)(DA)(DC)(DC)(DG)(DT)(DG)(DC) (DA)(DT)(DC)(DG) (DA)(DT)(DG)(DT)(DT) (DG)(DA)(DA)(DA)(DG)(DA)(DG)(DG)(DC)(DC) (DC)(DT)(DC)(DC)(DG) (DT)(DC)(DC)(DT) (DT)(DA)(DT)(DT)(DA)(DC)(DT)(DT)(DC)(DA) (DA)(DG)(DT)(DC)(DC)(DC) (DT)(DG)(DG) (DG)(DG)

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Macromolecule #6: Widom 603 DNA sequence

MacromoleculeName: Widom 603 DNA sequence / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.906613 KDa
SequenceString: (DC)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DA)(DC) (DT)(DT)(DG)(DA)(DA)(DG)(DT)(DA)(DA)(DT) (DA)(DA)(DG)(DG)(DA)(DC)(DG)(DG)(DA) (DG)(DG)(DG)(DC)(DC)(DT)(DC)(DT)(DT)(DT) (DC) (DA)(DA)(DC)(DA)(DT)(DC) ...String:
(DC)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DA)(DC) (DT)(DT)(DG)(DA)(DA)(DG)(DT)(DA)(DA)(DT) (DA)(DA)(DG)(DG)(DA)(DC)(DG)(DG)(DA) (DG)(DG)(DG)(DC)(DC)(DT)(DC)(DT)(DT)(DT) (DC) (DA)(DA)(DC)(DA)(DT)(DC)(DG)(DA) (DT)(DG)(DC)(DA)(DC)(DG)(DG)(DT)(DG)(DG) (DT)(DT) (DA)(DG)(DC)(DC)(DT)(DT)(DG) (DG)(DA)(DT)(DT)(DG)(DC)(DC)(DC)(DT)(DC) (DT)(DA)(DC) (DC)(DG)(DT)(DG)(DG)(DC) (DC)(DT)(DA)(DA)(DG)(DC)(DG)(DT)(DA)(DC) (DT)(DT)(DA)(DG) (DA)(DA)(DG)(DC)(DC) (DC)(DG)(DA)(DG)(DT)(DG)(DA)(DC)(DG)(DA) (DC)(DT)(DT)(DC)(DA) (DC)(DA)(DC)(DG) (DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DC)(DG)(DA) (DA)(DC)(DT) (DG)(DG)

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6611 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.0.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38918
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.3) / Details: CryoSPARC ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.3) / Details: CryoSPARC non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7vz4


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The DNA chains of the initial model (7VZ4) were replaced with mutate_bases tool of 3DNA v2.1 by only swapping the bases itself, while preserving the sugar-phosphate backbone geometry. Prior ...Details: The DNA chains of the initial model (7VZ4) were replaced with mutate_bases tool of 3DNA v2.1 by only swapping the bases itself, while preserving the sugar-phosphate backbone geometry. Prior to refinements, the set of adaptive restraints for the protein chains (distances and dihedral angles) was created in ISOLDE based on the initial model (7VZ4), along with hydrogen bond restraints for the DNA. ISOLDE refinement was followed by the PHENIX real space refinement, with the protein chains restrained to themselves and the DNA restrained with base-pair hydrogen bonds and planarity.
Output model

PDB-8rgm:
Cryo-EM structure of nucleosome containing Widom603 DNA

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