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

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Entry
Database: EMDB / ID: 6792
TitleCryo-EM structure of p300
Map dataCryo-EM structure of p300. Transcriptional coactivator p300 is a large, multidomain protein that possess (HAT) histone acetyltransferase activity.
Samplep300 protein:
Histone acetyltransferase p300
Function / homologyZinc finger, ZZ-type / Regulation of gene expression by Hypoxia-inducible Factor / 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. / Zinc finger, TAZ-type / Creb binding ...Zinc finger, ZZ-type / Regulation of gene expression by Hypoxia-inducible Factor / 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. / Zinc finger, TAZ-type / Creb binding / RORA activates gene expression / Polo-like kinase mediated events / Pre-NOTCH Transcription and Translation / PPARA activates gene expression / Formation of the beta-catenin:TCF transactivating complex / Zinc finger, RING/FYVE/PHD-type / Bromodomain signature. / Histone acetylation protein / NOTCH2 intracellular domain regulates transcription / Coactivator CBP, KIX domain superfamily / Nuclear receptor coactivator, CREB-bp-like, interlocking / Bromodomain, conserved site / CBP/p300-type histone acetyltransferase domain / TAZ domain superfamily / CREB-binding protein/p300, atypical RING domain / Bromodomain-like superfamily / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Domain of Unknown Function (DUF902) / Nuclear receptor coactivator, interlocking / CBP/p300, atypical RING domain superfamily / Coactivator CBP, KIX domain / Bromodomain / Zinc finger, ZZ type / TAZ zinc finger / KIX domain / NOTCH1 Intracellular Domain Regulates Transcription / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Constitutive Signaling by NOTCH1 PEST Domain Mutants / RUNX3 regulates NOTCH signaling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Regulation of TP53 Activity through Acetylation / Regulation of TP53 Activity through Methylation / PI5P Regulates TP53 Acetylation / Activation of the TFAP2 (AP-2) family of transcription factors / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of RUNX3 expression and activity / Dual incision in TC-NER / Bromodomain / RUNX3 regulates p14-ARF / NOTCH3 Intracellular Domain Regulates Transcription / NOTCH4 Intracellular Domain Regulates Transcription / Estrogen-dependent gene expression / TRAF3-dependent IRF activation pathway / TRAF6 mediated IRF7 activation / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Gap-filling DNA repair synthesis and ligation in TC-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / HATs acetylate histones / Attenuation phase / Transcriptional regulation of white adipocyte differentiation / SUMOylation of transcription cofactors / Circadian Clock / Histone acetyltransferase Rtt109/CBP / B-WICH complex positively regulates rRNA expression / Activation of anterior HOX genes in hindbrain development during early embryogenesis / CD209 (DC-SIGN) signaling / Metalloprotease DUBs / histone H2B acetylation / peptide butyryltransferase activity / protein propionyltransferase activity / peptidyl-lysine butyrylation / histone crotonyltransferase activity / histone butyryltransferase activity / peptidyl-lysine propionylation / peptidyl-lysine crotonylation / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / regulation of tubulin deacetylation / peptide-lysine-N-acetyltransferase activity / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / STAT family protein binding / regulation of androgen receptor signaling pathway / peptide N-acetyltransferase activity / positive regulation by host of viral transcription / positive regulation of gene expression, epigenetic / somitogenesis / internal protein amino acid acetylation / internal peptidyl-lysine acetylation / N-terminal peptidyl-lysine acetylation / pre-mRNA intronic binding / megakaryocyte development / positive regulation of transcription of Notch receptor target / macrophage derived foam cell differentiation / fat cell differentiation / Transferases, Acyltransferases, Transferring groups other than aminoacyl groups / beta-catenin-TCF complex assembly / transferase activity, transferring acyl groups
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 9.8 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: 5xzs

SummaryFull reportAbout validation report
DateDeposition: Jul 13, 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: 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-5xzs
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5xzs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6792.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
1.89 Å/pix.
= 120.96 Å
64 pix
1.89 Å/pix.
= 120.96 Å
64 pix
1.89 Å/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 Level:0.024 (by author), 0.024 (movie #1):
Minimum - Maximum-0.049451843 - 0.09365533
Average (Standard dev.)0.0026306694 (0.013315585)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin0.00.00.0
Limit63.063.063.0
Spacing646464
CellA=B=C: 120.96 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/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
NX/NY/NZ
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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