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- EMDB-46546: 147-bp 5S rDNA nucleosome - open I (open on the downstream side) -

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Basic information

Entry
Database: EMDB / ID: EMD-46546
Title147-bp 5S rDNA nucleosome - open I (open on the downstream side)
Map data147-bp 5S rDNA nucleosome - open I (open on the downstream side)
Sample
  • Complex: 147-bp 5S rDNA nucleosome - open I, downstream
    • Complex: 5S rDNA
      • DNA: 5S rDNA (noncoding strand)
      • DNA: 5S rDNA (coding strand)
    • Complex: Human core histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 2-A
      • Protein or peptide: Histone H2B type 1-M
Keywords5S rDNA nucleosome / natural nucleosome positioning sequence / DNA sequence-dependent breathing / GENE REGULATION / GENE REGULATION-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 / 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 / structural constituent of chromatin / 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 / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / 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 H4 / Histone H2A type 2-A / Histone H3.2 / Histone H2B type 1-M
Similarity search - Component
Biological speciesXenopus borealis (Kenyan clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAlegrio Louro J / Cruz-Becerra G / Kadonaga JT / Leschziner AE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM145296 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118060 United States
CitationJournal: Genes Dev / Year: 2025
Title: Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif.
Authors: Jaime Alegrio-Louro / Grisel Cruz-Becerra / George A Kassavetis / James T Kadonaga / Andres E Leschziner /
Abstract: The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally ...The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally determined. Here we used cryo-EM to show that both proteins bind to the nucleosome acidic patch via analogous arginine anchors with one molecule bound to each face of the nucleosome. We additionally used the natural promoter-containing 5S rDNA sequence for structural analysis of the nucleosome. These structures of an ancient nucleosome-binding motif suggest that there is an untapped realm of proteins with a related mode of binding to chromatin.
History
DepositionAug 11, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46546.png

Downloads & links

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Map

FileDownload / File: emd_46546.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation147-bp 5S rDNA nucleosome - open I (open on the downstream side)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 208 pix.
= 194.48 Å		0.94 Å/pix.
x 208 pix.
= 194.48 Å		0.94 Å/pix.
x 208 pix.
= 194.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.69842917 - 1.0089033
Average (Standard dev.)0.0014134373 (±0.037741117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 194.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_46546_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46546_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 147-bp 5S rDNA nucleosome - open I, downstream

EntireName: 147-bp 5S rDNA nucleosome - open I, downstream
Components
  • Complex: 147-bp 5S rDNA nucleosome - open I, downstream
    • Complex: 5S rDNA
      • DNA: 5S rDNA (noncoding strand)
      • DNA: 5S rDNA (coding strand)
    • Complex: Human core histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 2-A
      • Protein or peptide: Histone H2B type 1-M

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Supramolecule #1: 147-bp 5S rDNA nucleosome - open I, downstream

SupramoleculeName: 147-bp 5S rDNA nucleosome - open I, downstream / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
Molecular weightTheoretical: 110 KDa

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Supramolecule #2: 5S rDNA

SupramoleculeName: 5S rDNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)

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Supramolecule #3: Human core histones

SupramoleculeName: Human core histones / type: complex / ID: 3 / Parent: 1 / 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: 11.617591 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVGLFED TNLCAIHAKR VTIMPKDIQ LARRIRGERA

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: 9.279875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 2-A

MacromoleculeName: Histone H2A type 2-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.468418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSRSSRAGL QFPVGRVHRL LRKGNYAERV GAGAPVYMAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAIRNDEEL NKLLGKVTI AQGGVLPNIQ AVLLPK

UniProtKB: Histone H2A type 2-A

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Macromolecule #4: Histone H2B type 1-M

MacromoleculeName: Histone H2B type 1-M / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.493994 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSS

UniProtKB: Histone H2B type 1-M

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Macromolecule #5: 5S rDNA (noncoding strand)

MacromoleculeName: 5S rDNA (noncoding strand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
Molecular weightTheoretical: 38.058254 KDa
SequenceString: (DC)(DT)(DT)(DG)(DT)(DT)(DT)(DT)(DC)(DC) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DG)(DG)(DG) (DA)(DA)(DA)(DA)(DG)(DA)(DC)(DC)(DC) (DT)(DG)(DG)(DC)(DA)(DT)(DG)(DG)(DG)(DG) (DA) (DG)(DG)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DT)(DG)(DT)(DT)(DT)(DT)(DC)(DC) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DG)(DG)(DG) (DA)(DA)(DA)(DA)(DG)(DA)(DC)(DC)(DC) (DT)(DG)(DG)(DC)(DA)(DT)(DG)(DG)(DG)(DG) (DA) (DG)(DG)(DA)(DG)(DC)(DT)(DG)(DG) (DG)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DA) (DG)(DA) (DA)(DG)(DG)(DC)(DA)(DG)(DC) (DA)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DG) (DG)(DA)(DA) (DA)(DA)(DG)(DT)(DC)(DA) (DG)(DC)(DC)(DT)(DT)(DG)(DT)(DG)(DC)(DT) (DC)(DG)(DC)(DC) (DT)(DA)(DC)(DG)(DG) (DC)(DC)(DA)(DT)(DA)(DC)(DC)(DA)(DC)(DC) (DC)(DT)(DG)(DA)(DA) (DA)(DG)(DT)

GENBANK: GENBANK: V01426.1

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Macromolecule #6: 5S rDNA (coding strand)

MacromoleculeName: 5S rDNA (coding strand) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
Molecular weightTheoretical: 37.866066 KDa
SequenceString: (DA)(DC)(DT)(DT)(DT)(DC)(DA)(DG)(DG)(DG) (DT)(DG)(DG)(DT)(DA)(DT)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DG)(DG)(DC)(DG)(DA)(DG) (DC)(DA)(DC)(DA)(DA)(DG)(DG)(DC)(DT)(DG) (DA) (DC)(DT)(DT)(DT)(DT)(DC) ...String:
(DA)(DC)(DT)(DT)(DT)(DC)(DA)(DG)(DG)(DG) (DT)(DG)(DG)(DT)(DA)(DT)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DG)(DG)(DC)(DG)(DA)(DG) (DC)(DA)(DC)(DA)(DA)(DG)(DG)(DC)(DT)(DG) (DA) (DC)(DT)(DT)(DT)(DT)(DC)(DC)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DT)(DG)(DC) (DT)(DG) (DC)(DC)(DT)(DT)(DC)(DT)(DG) (DG)(DG)(DG)(DG)(DG)(DG)(DG)(DC)(DC)(DC) (DA)(DG)(DC) (DT)(DC)(DC)(DT)(DC)(DC) (DC)(DC)(DA)(DT)(DG)(DC)(DC)(DA)(DG)(DG) (DG)(DT)(DC)(DT) (DT)(DT)(DT)(DC)(DC) (DC)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DG)(DG) (DA)(DA)(DA)(DA)(DC) (DA)(DA)(DG)

GENBANK: GENBANK: V01426.1

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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

Concentration0.13 mg/mL
BufferpH: 7.6
Component:
ConcentrationName
23.0 mMHEPES-potassium
0.66 mMEDTA
77.0 mMPotassium chloride
0.0085 %(w/V)NP-40
11.0 mMSodium chloride
1.7 %(V/V)Glycerol
17.0 mMTris
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 5571 / Number real images: 5291 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
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

CTF correctionSoftware: (Name: cryoSPARC, RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80111
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab-initio job in cryoSPARC.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement job in cryoSPARC.
Final 3D classificationNumber classes: 10 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9d3s:
147-bp 5S rDNA nucleosome - open I (open on the downstream side)

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