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- PDB-5xzs: Cryo-EM structure of p300 -

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Entry
Database: PDB / ID: 5xzs
TitleCryo-EM structure of p300
ComponentsHistone acetyltransferase p300
KeywordsTRANSCRIPTION / transcriptional coactivator / HAT / auto-inhibited closed conformation
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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single 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, N.S. / Sengupta, J. / Roy, S. / Kundu, T.K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2017 / Release: Jan 23, 2019

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Assembly

Deposited unit
A: Histone acetyltransferase p300


Theoretical massNumber of molelcules
Total (without water)72,1001
Polyers72,1001
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300 / Coordinate model: Cα atoms only


Mass: 72100.062 Da / Num. of mol.: 1 / Fragment: UNP residues 1046-1664 / Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09472, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: p300 protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer ID
110 mMTris-Cl1
2150 mMNaCl1
31 mMDTT1
42 mMPMSF1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Calibrated magnification: 78894 / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4500 nm / Cs: 2 mm / C2 aperture diameter: 150 microns
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 15 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN22.12particle selectionparticles picked semiautomatically: both using e2boxer.py and manually
2SPIDERparticle selectionparticles picked in EMAN2 exported to SPIDER and also picked separately in SPIDER
3TIA4.7image acquisition
5EMAN22.12CTF correction
6SPIDERCTF correction
9UCSF Chimera1.11model fittingCrystal structure of 4BHW was fitted using Chimera
11EMAN22.12initial Euler assignment
12SPIDERfinal Euler assignment
13SPIDERclassification
14SPIDER3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 16152 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingPDB-ID: 4BHW
Pdb chain ID: A / Pdb chain residue range: 1046-1664
Least-squares processHighest resolution: 9.8 Å

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