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- EMDB-6792: Cryo-EM structure of p300 -

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Basic information

Entry
Database: EMDB / ID: EMD-6792
TitleCryo-EM structure of p300
Map data
Samplep300 protein:
Histone acetyltransferase p300
Function / homology
Function and homology information


histone H2B acetylation / histone butyryltransferase activity / peptidyl-lysine butyrylation / histone crotonyltransferase activity / peptidyl-lysine crotonylation / peptide butyryltransferase activity / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding ...histone H2B acetylation / histone butyryltransferase activity / peptidyl-lysine butyrylation / histone crotonyltransferase activity / peptidyl-lysine crotonylation / peptide butyryltransferase activity / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / swimming / regulation of tubulin deacetylation / thigmotaxis / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / STAT family protein binding / peptide-lysine-N-acetyltransferase activity / regulation of androgen receptor signaling pathway / positive regulation by host of viral transcription / internal peptidyl-lysine acetylation / positive regulation of gene expression, epigenetic / N-terminal peptidyl-lysine acetylation / internal protein amino acid acetylation / megakaryocyte development / face morphogenesis / transferase activity, transferring acyl groups / positive regulation of transcription of Notch receptor target / pre-mRNA intronic binding / fat cell differentiation / macrophage derived foam cell differentiation / platelet formation / beta-catenin-TCF complex assembly / protein acetylation / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein-containing complex assembly / acetyltransferase activity / histone H4 acetylation / positive regulation of Notch signaling pathway / somitogenesis / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / skeletal muscle tissue development / negative regulation of gluconeogenesis / histone acetylation / Transferases, Acyltransferases, Transferring groups other than aminoacyl groups / positive regulation of type I interferon production / activating transcription factor binding / histone acetyltransferase / histone acetyltransferase activity / regulation of autophagy / androgen receptor binding / RNA polymerase II activating transcription factor binding / B cell differentiation / nuclear hormone receptor binding / positive regulation of neuron projection development / regulation of megakaryocyte differentiation / protein destabilization / tau protein binding / animal organ morphogenesis / chromatin DNA binding / Notch signaling pathway / cellular response to UV / regulation of cell cycle / positive regulation of NIK/NF-kappaB signaling / regulation of transcription from RNA polymerase II promoter in response to hypoxia / nervous system development / regulation of cellular response to heat / RNA polymerase II transcription factor binding / transcription-coupled nucleotide-excision repair / lung development / beta-catenin binding / multicellular organism growth / circadian rhythm / protein-DNA complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / stimulatory C-type lectin receptor signaling pathway / chromosome / p53 binding / RNA polymerase II regulatory region sequence-specific DNA binding / transcription factor complex / heart development / positive regulation of DNA-binding transcription factor activity / positive regulation of protein binding / protein stabilization / transcription coactivator activity / regulation of signal transduction by p53 class mediator / response to estrogen / learning or memory / protein C-terminus binding / response to hypoxia / damaged DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein deubiquitination / apoptotic process / transcription factor binding / chromatin binding / regulation of transcription, DNA-templated / viral process
Zinc finger, RING/FYVE/PHD-type / Nuclear receptor coactivator, CREB-bp-like, interlocking / Bromodomain, conserved site / CBP/p300-type histone acetyltransferase domain / TAZ domain superfamily / Bromodomain-like superfamily / CREB-binding protein/p300, atypical RING domain / Nuclear receptor coactivator, interlocking / Coactivator CBP, KIX domain superfamily / Coactivator CBP, KIX domain ...Zinc finger, RING/FYVE/PHD-type / Nuclear receptor coactivator, CREB-bp-like, interlocking / Bromodomain, conserved site / CBP/p300-type histone acetyltransferase domain / TAZ domain superfamily / Bromodomain-like superfamily / CREB-binding protein/p300, atypical RING domain / Nuclear receptor coactivator, interlocking / Coactivator CBP, KIX domain superfamily / Coactivator CBP, KIX domain / Bromodomain / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Zinc finger, ZZ-type / Zinc finger, TAZ-type / CBP/p300, atypical RING domain superfamily / Histone acetyltransferase Rtt109/CBP
Histone acetyltransferase p300
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsGhosh R / Roy S / Sengupta J
CitationJournal: Biochemistry / Year: 2019
Title: Tumor Suppressor p53-Mediated Structural Reorganization of the Transcriptional Coactivator p300.
Authors: Raka Ghosh / Stephanie Kaypee / Manidip Shasmal / Tapas K Kundu / Siddhartha Roy / Jayati Sengupta /
Abstract: Transcriptional coactivator p300, a critical player in eukaryotic gene regulation, primarily functions as a histone acetyltransferase (HAT). It is also an important player in acetylation of a number ...Transcriptional coactivator p300, a critical player in eukaryotic gene regulation, primarily functions as a histone acetyltransferase (HAT). It is also an important player in acetylation of a number of nonhistone proteins, p53 being the most prominent one. Recruitment of p300 to p53 is pivotal in the regulation of p53-dependent genes. Emerging evidence suggests that p300 adopts an active conformation upon binding to the tetrameric p53, resulting in its enhanced acetylation activity. As a modular protein, p300 consists of multiple well-defined domains, where the structured domains are interlinked with unstructured linker regions. A crystal structure of the central domain of p300 encompassing Bromo, RING, PHD, and HAT domains demonstrates a compact module, where the HAT active site stays occluded by the RING domain. However, although p300 has a significant role in mediating the transcriptional activity of p53, only a few structural details on the complex of these two full-length proteins are available. Here, we present a cryo-electron microscopy (cryo-EM) study on the p300-p53 complex. The three-dimensional cryo-EM density map of the p300-p53 complex, when compared to the cryo-EM map of free p300, revealed that substantial change in the relative arrangement of Bromo and HAT domains occurs upon complex formation, which is likely required for exposing HAT active site and subsequent acetyltransferase activity. Our observation correlates well with previous studies showing that the presence of Bromodomain is obligatory for effective acetyltransferase activity of HAT. Thus, our result sheds new light on the mechanism whereby p300, following binding with p53, gets activated.
Validation ReportPDB-ID: 6k4n

SummaryFull reportAbout validation report
History
DepositionJul 13, 2017-
Header (metadata) releaseJan 23, 2019-
Map releaseJan 23, 2019-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6k4n
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6k4n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6792.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 64 pix.
= 120.96 Å
1.89 Å/pix.
x 64 pix.
= 120.96 Å
1.89 Å/pix.
x 64 pix.
= 120.96 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 LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.049451843 - 0.09365533
Average (Standard dev.)0.0026306694 (±0.013315585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 120.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z120.960120.960120.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0490.0940.003

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Supplemental data

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Sample components

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Entire p300 protein

EntireName: p300 protein / Number of components: 2

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Component #1: cellular-component, p300 protein

Cellular-componentName: p300 protein / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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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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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
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: 1500.0 - 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: 16152
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 9.8 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
Output model

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