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- EMDB-60156: Structure of free nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-60156
TitleStructure of free nucleosome
Map data
Sample
  • Complex: free nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
  • DNA: DNA (147-MER)
  • DNA: DNA (147-MER)
KeywordsNucleosome / histone / DNA / STRUCTURAL PROTEIN/DNA / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


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 ...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 / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / 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) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / Metalloprotease DUBs / 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 / UCH proteinases / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / heterochromatin formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / gene expression / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin binding / negative regulation of transcription by RNA polymerase II / 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 / Histone-fold
Similarity search - Domain/homology
Histone H2B type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXu K / Zhang Y / Yin Y / Xue W / Han Y / Tian Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32301018 China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5.
Authors: Wanqiang Xue / Yaoyao Han / Ying Tian / Junzheng Wang / Zhiyuan Xie / Xin Zheng / Xue Yue / Siqi Dong / Huimin Li / Zhen Luo / Siqiu Zhang / Ying Yang / Zhe Zou / Wei Li / Nana Ma / Fangjie ...Authors: Wanqiang Xue / Yaoyao Han / Ying Tian / Junzheng Wang / Zhiyuan Xie / Xin Zheng / Xue Yue / Siqi Dong / Huimin Li / Zhen Luo / Siqiu Zhang / Ying Yang / Zhe Zou / Wei Li / Nana Ma / Fangjie Zhu / Chunlai Chen / Yimeng Yin / Yixiao Zhang / Ke Xu /
Abstract: Among the regulatory factor X (RFX) transcription factor family, RFX5 is uniquely reported to bind nucleosomes and induce nucleosome remodeling in vivo. Dysfunctions in RFX5 have been implicated in ...Among the regulatory factor X (RFX) transcription factor family, RFX5 is uniquely reported to bind nucleosomes and induce nucleosome remodeling in vivo. Dysfunctions in RFX5 have been implicated in various diseases. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the RFX5-nucleosome complex, revealing that the extended DNA binding domain (eDBD) of RFX5 binds to the nucleosome at superhelical location +2. RFX5 eDBD engages not only with nucleosomal DNA but also with histones through extensive interactions. Compared to the structure of a free nucleosome, RFX5 eDBD induces localized distortion of the bound DNA gyre and detachment of the adjacent DNA gyre in the RFX5-nucleosome complex. This structural alteration could potentially increase DNA accessibility and enhance transcriptional activity in vivo. Overall, our study provides novel insights into the mechanisms by which RFX5 eDBD interacts with and destabilizes nucleosomes.
History
DepositionMay 15, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60156.png

Downloads & links

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Map

FileDownload / File: emd_60156.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 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: 0.426
Minimum - Maximum-2.2305863 - 3.8334095
Average (Standard dev.)0.0019530061 (±0.071183555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.49997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60156_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60156_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60156_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 : free nucleosome

EntireName: free nucleosome
Components
  • Complex: free nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
  • DNA: DNA (147-MER)
  • DNA: DNA (147-MER)

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Supramolecule #1: free nucleosome

SupramoleculeName: free nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.543203 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPMARTKQTA RKSTGGKAPR KQLATKAARK SAPATGGVKK PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQS SAVMALQEAS EAYLVGLFED TNLAAIHAKR VTIMPKDIQL ARRIRGERA

UniProtKB: Histone H3.2

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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: 11.824946 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MADLMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG

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: 14.319716 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPMSGRGKQG GKARAKAKTR SSRAGLQFPV GRVHRLLRKG NYSERVGAGA PVYLAAVLEY LTAEILELAG NAARDNKKTR IIPRHLQLA IRNDEELNKL LGRVTIAQGG VLPNIQAVLL PKKTESHHKA KGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.351734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MADLMPEPAK SAPAPKKGSK KAVTKAQKKD GKKRKRSRKE SYSVYVYKVL KQVHPDTGIS SKAMGIMNSF VNDIFERIAG EASRLAHYN KRSTITSREI QTAVRLLLPG ELAKHAVSEG TKAVTKYTSA K

UniProtKB: Histone H2B type 1-K

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.664109 KDa
SequenceString: (DA)(DT)(DC)(DC)(DA)(DC)(DA)(DC)(DG)(DT) (DT)(DA)(DC)(DA)(DC)(DG)(DA)(DC)(DG)(DC) (DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DT)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG) (DT)(DG)(DC)(DA)(DA)(DG) ...String:
(DA)(DT)(DC)(DC)(DA)(DC)(DA)(DC)(DG)(DT) (DT)(DA)(DC)(DA)(DC)(DG)(DA)(DC)(DG)(DC) (DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DT)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG) (DT)(DG)(DC)(DA)(DA)(DG)(DC)(DA) (DT)(DG)(DA)(DT)(DC)(DC)(DC)(DT)(DT)(DC) (DG)(DA) (DT)(DG)(DA)(DA)(DT)(DA)(DG) (DA)(DG)(DC)(DC)(DG)(DA)(DC)(DT)(DG)(DG) (DG)(DC)(DA) (DT)(DA)(DG)(DT)(DA)(DA) (DC)(DG)(DC)(DG)(DT)(DG)(DG)(DG)(DT)(DT) (DG)(DG)(DT)(DG) (DA)(DG)(DG)(DT)(DG) (DG)(DT)(DT)(DC)(DA)(DC)(DG)(DG)(DT)(DC) (DA)(DT)(DG)(DC)(DC) (DG)(DC)(DT)(DT) (DG)(DG)(DG)(DT)(DA)(DA)(DG)(DC)(DA)(DG) (DA)(DT)(DC)(DG)(DG)(DA) (DA)(DG)(DA) (DG)(DG)(DA)(DT)

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.08177 KDa
SequenceString: (DA)(DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC)(DC) (DG)(DA)(DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA) (DC)(DC)(DC)(DA)(DA)(DG)(DC)(DG)(DG) (DC)(DA)(DT)(DG)(DA)(DC)(DC)(DG)(DT)(DG) (DA) (DA)(DC)(DC)(DA)(DC)(DC) ...String:
(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC)(DC) (DG)(DA)(DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA) (DC)(DC)(DC)(DA)(DA)(DG)(DC)(DG)(DG) (DC)(DA)(DT)(DG)(DA)(DC)(DC)(DG)(DT)(DG) (DA) (DA)(DC)(DC)(DA)(DC)(DC)(DT)(DC) (DA)(DC)(DC)(DA)(DA)(DC)(DC)(DC)(DA)(DC) (DG)(DC) (DG)(DT)(DT)(DA)(DC)(DT)(DA) (DT)(DG)(DC)(DC)(DC)(DA)(DG)(DT)(DC)(DG) (DG)(DC)(DT) (DC)(DT)(DA)(DT)(DT)(DC) (DA)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DA) (DT)(DC)(DA)(DT) (DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DA)(DA)(DG)(DA)(DT) (DC)(DG)(DG)(DA) (DA)(DG)(DA)(DG)(DC)(DG)(DT)(DC)(DG)(DT) (DG)(DT)(DA)(DA)(DC)(DG) (DT)(DG)(DT) (DG)(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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6pwe

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 231337
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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