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- EMDB-33535: Cryo-EM structure of the nucleosome in complex with p53 -

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Entry
Database: EMDB / ID: EMD-33535
TitleCryo-EM structure of the nucleosome in complex with p53
Map dataCryo-EM structure of the nucleosome in complex with p53
Sample
  • Complex: Cryo-EM structure of the nucleosome in complex with p53
    • Complex: nucleosome, p53
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Cellular tumor antigen p53
    • Complex: DNA
      • DNA: DNA (169-MER)
      • DNA: DNA (169-MER)
KeywordsTranscription factor / Tumor-suppressor / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / negative regulation of megakaryocyte differentiation / hematopoietic progenitor cell differentiation / protein localization to CENP-A containing chromatin / core promoter sequence-specific DNA binding / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / negative regulation of stem cell proliferation / CENP-A containing nucleosome / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / Packaging Of Telomere Ends / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Recognition and association of DNA glycosylase with site containing an affected purine
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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
Cellular tumor antigen p53 / 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: 4.07 Å
AuthorsNishimura M / Nozawa K / Takizawa Y / Kurumizaka H
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19J23094 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Society for the Promotion of Science (JSPS)JP20K06599 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05154 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101076 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
Japan Science and TechnologyJPMJPR18K9 Japan
Japan Science and TechnologyJPMJER1901 Japan
CitationJournal: PNAS Nexus / Year: 2022
Title: Structural basis for p53 binding to its nucleosomal target DNA sequence.
Authors: Masahiro Nishimura / Yoshimasa Takizawa / Kayo Nozawa / Hitoshi Kurumizaka /
Abstract: The tumor suppressor p53 functions as a pioneer transcription factor that binds a nucleosomal target DNA sequence. However, the mechanism by which p53 binds to its target DNA in the nucleosome ...The tumor suppressor p53 functions as a pioneer transcription factor that binds a nucleosomal target DNA sequence. However, the mechanism by which p53 binds to its target DNA in the nucleosome remains elusive. Here we report the cryo-electron microscopy structures of the p53 DNA-binding domain and the full-length p53 protein complexed with a nucleosome containing the 20 base-pair target DNA sequence of p53 (p53BS). In the p53-nucleosome structures, the p53 DNA-binding domain forms a tetramer and specifically binds to the p53BS DNA, located near the entry/exit region of the nucleosome. The nucleosomal position of the p53BS DNA is within the genomic p21 promoter region. The p53 binding peels the DNA from the histone surface, and drastically changes the DNA path around the p53BS on the nucleosome. The C-terminal domain of p53 also binds to the DNA around the center and linker DNA regions of the nucleosome, as revealed by hydroxyl radical footprinting. These results provide important structural information for understanding the mechanism by which p53 binds the nucleosome and changes the chromatin structure for gene activation.
History
DepositionJun 3, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33535.png

Downloads & links

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Map

FileDownload / File: emd_33535.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the nucleosome in complex with p53
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.014779729 - 0.04909714
Average (Standard dev.)0.00028280567 (±0.0019023193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33535_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33535_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the nucleosome in complex with p53

EntireName: Cryo-EM structure of the nucleosome in complex with p53
Components
  • Complex: Cryo-EM structure of the nucleosome in complex with p53
    • Complex: nucleosome, p53
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Cellular tumor antigen p53
    • Complex: DNA
      • DNA: DNA (169-MER)
      • DNA: DNA (169-MER)

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Supramolecule #1: Cryo-EM structure of the nucleosome in complex with p53

SupramoleculeName: Cryo-EM structure of the nucleosome in complex with p53
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 398 KDa

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Supramolecule #2: nucleosome, p53

SupramoleculeName: nucleosome, p53 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #7

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone 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

UniProtKB: Histone H3.1

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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: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

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: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Cellular tumor antigen p53

MacromoleculeName: Cellular tumor antigen p53 / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.855297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMEEPQSDP SVEPPLSQET FSDLWKLLPE NNVLSPLPSQ AMDDLMLSPD DIEQWFTEDP GPDEAPRMPE AAPPVAPAPA APTPAAPAP APSWPLSSSV PSQKTYQGSY GFRLGFLHSG TAKSVTCTYS PALNKMFCQL AKTCPVQLWV DSTPPPGTRV R AMAIYKQS ...String:
GSMEEPQSDP SVEPPLSQET FSDLWKLLPE NNVLSPLPSQ AMDDLMLSPD DIEQWFTEDP GPDEAPRMPE AAPPVAPAPA APTPAAPAP APSWPLSSSV PSQKTYQGSY GFRLGFLHSG TAKSVTCTYS PALNKMFCQL AKTCPVQLWV DSTPPPGTRV R AMAIYKQS QHMTEVVRRC PHHERCSDSD GLAPPQHLIR VEGNLRVEYL DDRNTFRHSV VVPYEPPEVG SDCTTIHYNY MC NSSCMGG MNRRPILTII TLEDSSGNLL GRNSFEVRVC ACPGRDRRTE EENLRKKGEP HHELPPGSTK RALPNNTSSS PQP KKKPLD GEYFTLQIRG RERFEMFREL NEALELKDAQ AGKEPGGSRA HSSHLKSKKG QSTSRHKKLM FKTEGPDSD

UniProtKB: Cellular tumor antigen p53

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Macromolecule #5: DNA (169-MER)

MacromoleculeName: DNA (169-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.032137 KDa
SequenceString: (DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(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) ...String:
(DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(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)(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)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT) (DA)(DG)(DG)(DG)(DC)(DA) (DT)(DG)(DT) (DC)(DC)(DG)(DG)(DG)(DC)(DA)(DT)(DG)(DT) (DC)(DC)(DC)(DG)(DA)(DA)(DA) (DT)(DT) (DC)(DA)(DT)(DA)(DG)(DA)(DT)

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Macromolecule #6: DNA (169-MER)

MacromoleculeName: DNA (169-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.312316 KDa
SequenceString: (DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DG)(DG)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DG)(DA)(DC)(DA) (DT)(DG)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC) ...String:
(DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DG)(DG)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DG)(DA)(DC)(DA) (DT)(DG)(DC)(DC)(DC)(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)(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)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG) (DG)(DA) (DT)(DT)(DC)(DT)(DC)(DA)(DG)

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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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC8H19KN2O5SHEPES-KOH
2.0 mMC9H15O6PTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2739901
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 92142
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7ohc

source_name: PDB, initial_model_type: experimental model

3kmd

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL
Output model

PDB-7xzz:
Cryo-EM structure of the nucleosome in complex with p53

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