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- EMDB-53535: p53 bound to nucleosome at position SHL+5.9 (non-crosslinked samp... -

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Basic information

Entry
Database: EMDB / ID: EMD-53535
Titlep53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, focus refined map of p53)
Map dataUnfiltered unsharpened map
Sample
  • Complex: p53 in complex with a nucleosome
    • Complex: Nucleosome core particle
      • Protein or peptide: H3.1
      • Protein or peptide: H4
      • Protein or peptide: H2A
      • Protein or peptide: H2B
      • DNA: DNA-for
      • DNA: DNA-rev
    • Complex: p53 tetramer
      • Protein or peptide: p53
KeywordsTumour-suppressor / transcription factor / GENE REGULATION
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChakraborty D / Kater L / Kempf G / Cavadini S / Thoma NH
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
Other private
Other private
CitationJournal: To Be Published
Title: p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, focus refined map of p53)
Authors: Na NA
History
DepositionApr 30, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53535.png

Downloads & links

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Map

FileDownload / File: emd_53535.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 384 pix.
= 432.64 Å		1.13 Å/pix.
x 384 pix.
= 432.64 Å		1.13 Å/pix.
x 384 pix.
= 432.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.352
Minimum - Maximum-0.8054491 - 1.6091892
Average (Standard dev.)-0.0002071582 (±0.022488015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 432.64014 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_53535_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53535_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_53535_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : p53 in complex with a nucleosome

EntireName: p53 in complex with a nucleosome
Components
  • Complex: p53 in complex with a nucleosome
    • Complex: Nucleosome core particle
      • Protein or peptide: H3.1
      • Protein or peptide: H4
      • Protein or peptide: H2A
      • Protein or peptide: H2B
      • DNA: DNA-for
      • DNA: DNA-rev
    • Complex: p53 tetramer
      • Protein or peptide: p53

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Supramolecule #1: p53 in complex with a nucleosome

SupramoleculeName: p53 in complex with a nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6

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Supramolecule #3: p53 tetramer

SupramoleculeName: p53 tetramer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7

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Macromolecule #1: H3.1

MacromoleculeName: H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

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Macromolecule #2: H4

MacromoleculeName: H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

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Macromolecule #3: H2A

MacromoleculeName: H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

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Macromolecule #4: H2B

MacromoleculeName: H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.088336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSA

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Macromolecule #7: p53

MacromoleculeName: p53 / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.711176 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMEEPQS DPSVEPPLSQ ETFSDLWKLL PENNVLSPLP SQAMDDLMLS PDDIEQWFTE DPGPDEAPRM PEAAPPVAPA PAAPTPAAPA PAPSWPLSSS VPSQKTYQGS YGFRLGFLHS GTAKSVTCTY SPALNKMFCQ LAKTCPVQLW ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMEEPQS DPSVEPPLSQ ETFSDLWKLL PENNVLSPLP SQAMDDLMLS PDDIEQWFTE DPGPDEAPRM PEAAPPVAPA PAAPTPAAPA PAPSWPLSSS VPSQKTYQGS YGFRLGFLHS GTAKSVTCTY SPALNKMFCQ LAKTCPVQLW VDSTPPPGTR VRAMAIYKQS QHMTEVVRRC PHHERCSDSD GLAPPQHLIR VEGNLRVEYL DDRNTFRHSV VVPYEPPEVG SDCTTIHYNY MCNSSCMGGM NRRPILTIIT LEDSSGNLLG RNSFEVRVCA CPGRDRRTEE ENLRKKGEPH HELPPGSTKR ALPNNTSSSP QPKKKPLDGE YFTLQIRGRE RFEMFRELNE ALELKDAQAG KEPGGSRAHS SHLKSKKGQS TSRHKKLMFK TEGPDSD

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Macromolecule #5: DNA-for

MacromoleculeName: DNA-for / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.960898 KDa
SequenceString: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DC)(DT) (DG)(DC)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA) ...String:
(DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DC)(DT) (DG)(DC)(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) (DT)(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)(DA)(DA)(DC)(DA)(DT)(DG)(DC) (DC)(DC)(DG)(DG)(DG)(DC) (DA)(DT)(DG) (DT)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT)

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Macromolecule #6: DNA-rev

MacromoleculeName: DNA-rev / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.499238 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA) (DC)(DA)(DT)(DG)(DC)(DC)(DC)(DG)(DG)(DG) (DC)(DA)(DT)(DG)(DT)(DT)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA) (DC)(DA)(DT)(DG)(DC)(DC)(DC)(DG)(DG)(DG) (DC)(DA)(DT)(DG)(DT)(DT)(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)(DA)(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)(DG)(DC)(DA) (DG)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163724
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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