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- EMDB-64640: Cryo-EM structure of the nucleosome core particle with site-speci... -

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Entry
Database: EMDB / ID: EMD-64640
TitleCryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking
Map data
Sample
  • Complex: Human canonical histone and 601 DNA
    • Complex: Human canonical histone with mutantion C96S/C110S/K115C
      • Complex: Histone H3.1
        • Protein or peptide: Histone H3.1
      • Complex: Histone H3.1
        • Protein or peptide: Histone H3.1
      • Complex: Histone H4
        • Protein or peptide: Histone H4
      • Complex: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2A type 1-B/E
      • Complex: Histone H2B type 1-J
        • Protein or peptide: Histone H2B type 1-J
    • Complex: 601 DNA with an alkynyl-dU modification at position 74 and a Cy5 fluorophore
      • DNA: DNA (145-MER)
      • DNA: DNA (145-MER)
KeywordsHistone / Nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / epigenetic regulation of gene expression / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / 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 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / Metalloprotease DUBs / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / nucleosome assembly / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / HATs acetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / killing of cells of another organism / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
: / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2A conserved site / Histone H2A signature. / Histone H2B 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: 3.24 Å
AuthorsZhou CZ / Li HT / Shan XJ / Ji GY
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377059 China
Not funded2023YFA0913800 China
CitationJournal: Protein Cell / Year: 2025
Title: DNA - histone cross-link locks the nucleosome structure and disrupts its recognition and processing.
Authors: Xiajing Shan / Gaoyuan Ji / Jiahui Li / Mengtian Ren / Jingke Ma / Yifei Zhou / Haitao Li / Chuanzheng Zhou /
Abstract: DNA-histone cross-links (DHCs) frequently arise within nucleosomes during DNA damage and repair processes. However, the functional consequences of DHC within nucleosomes remain largely unexplored. In ...DNA-histone cross-links (DHCs) frequently arise within nucleosomes during DNA damage and repair processes. However, the functional consequences of DHC within nucleosomes remain largely unexplored. In this study, we prepared structurally homogeneous nucleosomes containing a single, site-specific DHC using click chemistry and systematically evaluated the impact of DHC on nucleosome structure and function. Our results show that DHC markedly enhances nucleosome thermal stability and completely blocks both thermally induced passive sliding and chromatin remodeler-mediated active sliding. Moreover, DHC obstructs SP6 RNA polymerase-driven transcription elongation through nucleosomes, leading to premature termination approximately 15 bp upstream of the cross-linking site. DHC also increases histone resistance to proteolytic digestion within nucleosomes. These findings suggest that even a single DHC can substantially lock and rigidify the nucleosome structure and broadly interfere with the recognition and processing of nucleosomes by various cellular machineries, thereby rendering DHC a highly toxic and persistent form of DNA damage. This in vitro study highlights the unique impact of DHC on nucleosome architecture and is expected to motivate further exploration of its biological roles in vivo.
History
DepositionMay 16, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64640.png

Downloads & links

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Map

FileDownload / File: emd_64640.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-4.7296667 - 8.130012000000001
Average (Standard dev.)0.021586617 (±0.23679727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64640_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_64640_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human canonical histone and 601 DNA

EntireName: Human canonical histone and 601 DNA
Components
  • Complex: Human canonical histone and 601 DNA
    • Complex: Human canonical histone with mutantion C96S/C110S/K115C
      • Complex: Histone H3.1
        • Protein or peptide: Histone H3.1
      • Complex: Histone H3.1
        • Protein or peptide: Histone H3.1
      • Complex: Histone H4
        • Protein or peptide: Histone H4
      • Complex: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2A type 1-B/E
      • Complex: Histone H2B type 1-J
        • Protein or peptide: Histone H2B type 1-J
    • Complex: 601 DNA with an alkynyl-dU modification at position 74 and a Cy5 fluorophore
      • DNA: DNA (145-MER)
      • DNA: DNA (145-MER)

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Supramolecule #1: Human canonical histone and 601 DNA

SupramoleculeName: Human canonical histone and 601 DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: Human canonical histone with mutantion C96S/C110S/K115C

SupramoleculeName: Human canonical histone with mutantion C96S/C110S/K115C
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 601 DNA with an alkynyl-dU modification at position 74 and a Cy5 ...

SupramoleculeName: 601 DNA with an alkynyl-dU modification at position 74 and a Cy5 fluorophore
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7

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Supramolecule #4: Histone H3.1

SupramoleculeName: Histone H3.1 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #1
Details: H3 mutant, H3-C96S/C110S/K115C, in which Cys96 and Cys110 were substituted with Ser, leaving Cys115 as the sole reactive thiol
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Histone H3.1

SupramoleculeName: Histone H3.1 / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #2
Details: H3 mutant, H3-C96S/C110S/K115C, in which Cys96 and Cys110 were substituted with Ser, leaving Cys115 as the sole reactive thiol that is crosslinked
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 6 / Parent: 2 / Macromolecule list: #3 / Details: Recombinantly expressed human histone H4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Histone H2A type 1-B/E

SupramoleculeName: Histone H2A type 1-B/E / type: complex / ID: 7 / Parent: 2 / Macromolecule list: #4 / Details: Recombinantly expressed human histone H2A.2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: Histone H2B type 1-J

SupramoleculeName: Histone H2B type 1-J / type: complex / ID: 8 / Parent: 2 / Macromolecule list: #5 / Details: Recombinantly expressed human histone H2B.1
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.247801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL SAIHACRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.304852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL SAIHA(YCM)RVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.1

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #5: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 5 / 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 #6: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.00766 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DG) (DA)(DT)

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Macromolecule #7: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.505371 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

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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

Concentration0.18 mg/mL
BufferpH: 7.6 / Component - Concentration: 10.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HESPS / Details: 10 mM HEPES, pH 7.6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: PDC-32G Plasma Cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Detailscross-linked nucleosome via CuAAC method

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number real images: 1978 / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 64000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
Particle selectionNumber selected: 1081772
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8jbx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 199160
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Image recording ID2
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8jbx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199160
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8jbx


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9uz7:
Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking

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