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- EMDB-46541: 167-bp 5S rDNA nucleosome cross-linked with formaldehyde (stretch... -

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Basic information

Entry
Database: EMDB / ID: EMD-46541
Title167-bp 5S rDNA nucleosome cross-linked with formaldehyde (stretched due to preferential views but relevant for assessing DNA flexibility)
Map data167-bp 5S rDNA nucleosome cross-linked with formaldehyde (stretched due to preferential views but relevant for assessing DNA flexibility)
Sample
  • Complex: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with formaldehyde
    • 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 H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A2A
      • Protein or peptide: Histone H2A2A
      • Protein or peptide: Histone H2B1C
      • Protein or peptide: Histone H2B1C
Keywords5S rDNA nucleosome / natural nucleosome positioning sequence / formaldehyde / cross-linking / GENE REGULATION
Biological speciesXenopus borealis (Kenyan clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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: To Be Published
Title: Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif
Authors: Alegrio Louro J / Cruz-Becerra G / Kadonaga JT / Leschziner AE
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_46541.png

Downloads & links

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Map

FileDownload / File: emd_46541.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation167-bp 5S rDNA nucleosome cross-linked with formaldehyde (stretched due to preferential views but relevant for assessing DNA flexibility)
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: 0.101
Minimum - Maximum-0.77209747 - 1.1381042
Average (Standard dev.)0.0014284101 (±0.03400859)
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_46541_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_46541_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 : Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human...

EntireName: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with formaldehyde
Components
  • Complex: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with formaldehyde
    • 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 H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A2A
      • Protein or peptide: Histone H2A2A
      • Protein or peptide: Histone H2B1C
      • Protein or peptide: Histone H2B1C

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Supramolecule #1: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human...

SupramoleculeName: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with formaldehyde
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: #1-#2
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: #3-#10
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5S rDNA (noncoding strand)

MacromoleculeName: 5S rDNA (noncoding strand) / type: dna / ID: 1 / Classification: DNA
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
SequenceString:
TCAAGGCCGG GCTTGTTTT CCTGCCTGGG GGAAAAGACC CTGGCATGGG GAGGAGCTGG GCCCCCCCCA GAAGGCAGCA CAAGGGGAGG AAAAGTCAGC CTTGTGCTCG CCTACGGCCA TACCACCCTG AAAGTGCCCG ATATCGTCTG ATCTCGGA A GCCAAGCAG

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Macromolecule #2: 5S rDNA (coding strand)

MacromoleculeName: 5S rDNA (coding strand) / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
SequenceString:
CTGCTTGGCT TCCGAGATCA GACGATATCG GGCACTTTCA GGGTGGTATG GCCGTAGGCG AGCACAAGGC TGACTTTTCC TCCCCTTGTG CTGCCTTCTG GGGGGGGCCC AGCTCCTCCC CATGCCAGGG TCTTTTCCCC CAGGCAGGAA AACAAGCCCG GCCTTGA

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDF KTDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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Macromolecule #4: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDF KTDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #7: Histone H2A2A

MacromoleculeName: Histone H2A2A / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

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Macromolecule #8: Histone H2A2A

MacromoleculeName: Histone H2A2A / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

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Macromolecule #9: Histone H2B1C

MacromoleculeName: Histone H2B1C / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

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Macromolecule #10: Histone H2B1C

MacromoleculeName: Histone H2B1C / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

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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
1.0 %(m/V)Formaldehyde
23.0 mMHEPES-potassium
0.65 mMEDTA
0.0085 %(w/V)NP-40
77.0 mMPotassium chloride
31.0 mMSodium chloride
1.9 %(V/V)Glycerol
50.0 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: 6443 / Number real images: 6280 / 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: THE REPORTED RESOLUTION IS LIKELY OVERESTIMATED DUE TO PREFERENTIAL VIEWS.
Number images used: 224003
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: 2 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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