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- EMDB-6791: Cryo-EM structure of p300-p53 protein complex -

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Entry
Database: EMDB / ID: 6791
TitleCryo-EM structure of p300-p53 protein complex
Map dataCryo-EM map of p300-p53 complex. p53 protein is a homotetrameric tumor suppresor. Transcriptional coactivator p300 is a multidomain protein with HAT (histone acetyltransferase) activity.
Samplep300-p53 complex:
Histone acetyltransferase p300 / Cellular tumor antigen p53P53
Function / homologyBromodomain / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / RORA activates gene expression / p53, DNA-binding domain / p53, tetramerisation domain / Activation of PUMA and translocation to mitochondria / Polo-like kinase mediated events / Pre-NOTCH Transcription and Translation / p53 tumour suppressor family / PPARA activates gene expression ...Bromodomain / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / RORA activates gene expression / p53, DNA-binding domain / p53, tetramerisation domain / Activation of PUMA and translocation to mitochondria / Polo-like kinase mediated events / Pre-NOTCH Transcription and Translation / p53 tumour suppressor family / PPARA activates gene expression / Formation of the beta-catenin:TCF transactivating complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / NOTCH1 Intracellular Domain Regulates Transcription / NOTCH2 intracellular domain regulates transcription / Oxidative Stress Induced Senescence / Oncogene Induced Senescence / p53/RUNT-type transcription factor, DNA-binding domain superfamily / DNA Damage/Telomere Stress Induced Senescence / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / CREB-binding protein/p300, atypical RING domain / HATs acetylate histones / SUMOylation of transcription factors / Autodegradation of the E3 ubiquitin ligase COP1 / Transcriptional regulation of white adipocyte differentiation / SUMOylation of transcription cofactors / Association of TriC/CCT with target proteins during biosynthesis / Circadian Clock / B-WICH complex positively regulates rRNA expression / Regulation of gene expression by Hypoxia-inducible Factor / Activation of NOXA and translocation to mitochondria / CD209 (DC-SIGN) signaling / Domain of Unknown Function (DUF902) / TAZ domain superfamily / Bromodomain-like superfamily / Coactivator CBP, KIX domain superfamily / p53-like tetramerisation domain superfamily / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Bromodomain, conserved site / CBP/p300, atypical RING domain superfamily / Bromodomain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Zinc finger, ZZ type / P53 DNA-binding domain / TAZ zinc finger / KIX domain / P53 tetramerisation motif / Zinc finger, RING/FYVE/PHD-type / p53 transactivation domain / Histone acetylation protein / P53 transactivation motif / Histone acetyltransferase Rtt109/CBP / Creb binding / p53 family signature. / Bromodomain signature. / Zinc finger ZZ-type signature. / Bromodomain profile. / Zinc finger TAZ-type profile. / Zinc finger ZZ-type profile. / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Attenuation phase / TP53 Regulates Metabolic Genes / Activation of the TFAP2 (AP-2) family of transcription factors / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Expression / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Association with Co-factors / Regulation of TP53 Activity through Methylation / PI5P Regulates TP53 Acetylation / G2/M DNA damage checkpoint / G2/M Checkpoints / Stabilization of p53 / Transcriptional activation of cell cycle inhibitor p21 / The role of GTSE1 in G2/M progression after G2 checkpoint / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / TP53 Regulates Transcription of Caspase Activators and Caspases / NOTCH4 Intracellular Domain Regulates Transcription / Factors involved in megakaryocyte development and platelet production / Zinc finger, ZZ-type / TRAF6 mediated IRF7 activation / TRAF3-dependent IRF activation pathway / Zinc finger, TAZ-type / Estrogen-dependent gene expression / Coactivator CBP, KIX domain / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / NOTCH3 Intracellular Domain Regulates Transcription / RUNX3 regulates p14-ARF / Regulation of PTEN gene transcription / Regulation of RUNX3 expression and activity / RUNX3 regulates NOTCH signaling / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Regulation of TP53 Activity through Acetylation / CBP/p300-type histone acetyltransferase domain
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 10.7 Å resolution
AuthorsGhosh R / Roy S / Sengupta J
CitationJournal: To Be Published
Title: (manuscript in preparation) Title: p53-mediated Allosteric Activation of p300 Autoacetylation: Implications for Specificity of Gene Regulation
Authors: Kaypee S / Ghosh R / SA S / Shasmal M / Ghosh P / Roy NS / Sengupta J / Roy S / Kundu TK
Validation ReportPDB-ID: 5xzc

SummaryFull reportAbout validation report
DateDeposition: Jul 12, 2017 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.89
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.89
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5xzc
  • Surface level: 1.89
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5xzc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6791.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
1.89 Å/pix.
= 241.92 Å
128 pix
1.89 Å/pix.
= 241.92 Å
128 pix
1.89 Å/pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density
Contour Level:1.89 (by author), 1.89 (movie #1):
Minimum - Maximum-2.5380216 - 6.996958
Average (Standard dev.)0.1593592 (0.7202969)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin0.00.00.0
Limit127.0127.0127.0
Spacing128128128
CellA=B=C: 241.92 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z241.920241.920241.920
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-2.5386.9970.159

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Supplemental data

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Sample components

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Entire p300-p53 complex

EntireName: p300-p53 complex
Details: Proteins were purified separately and then complex was made for cryo-EM.
Number of components: 3

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Component #1: protein, p300-p53 complex

ProteinName: p300-p53 complex
Details: Proteins were purified separately and then complex was made for cryo-EM.
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Histone acetyltransferase p300

ProteinName: Histone acetyltransferase p300 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.100062 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Cellular tumor antigen p53

ProteinName: Cellular tumor antigen p53P53 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 29.898908 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 279 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 78894.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1700.0 - 4500.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 10088
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 10.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 4BHW
Chain ID: A
Modeling #2Input PDB model: 3KMD, 1C26
Output model

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