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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 dataCryo-EM structure of p300. Transcriptional coactivator p300 is a large, multidomain protein that possess (HAT) histone acetyltransferase activity.
Sample
  • Organelle or cellular component: p300 protein
    • Protein or peptide: Histone acetyltransferase p300
Function / homology
Function and homology information


behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity ...behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / NOTCH2 intracellular domain regulates transcription / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / histone H3 acetyltransferase activity / histone H4 acetyltransferase activity / cellular response to L-leucine / internal peptidyl-lysine acetylation / NFE2L2 regulating ER-stress associated genes / histone H3K27 acetyltransferase activity / peptide N-acetyltransferase activity / histone H3K18 acetyltransferase activity / acetylation-dependent protein binding / STAT3 nuclear events downstream of ALK signaling / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / Polo-like kinase mediated events / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / NFE2L2 regulates pentose phosphate pathway genes / regulation of androgen receptor signaling pathway / NFE2L2 regulating MDR associated enzymes / positive regulation by host of viral transcription / regulation of mitochondrion organization / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / TRAF6 mediated IRF7 activation / platelet formation / megakaryocyte development / peptide-lysine-N-acetyltransferase activity / nuclear androgen receptor binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / macrophage derived foam cell differentiation / regulation of tubulin deacetylation / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / STAT family protein binding / internal protein amino acid acetylation / acyltransferase activity / protein acetylation / fat cell differentiation / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of transforming growth factor beta receptor signaling pathway / PI5P Regulates TP53 Acetylation / acetyltransferase activity / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / RUNX3 regulates p14-ARF / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Attenuation phase / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / pre-mRNA intronic binding / somitogenesis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of cellular response to heat / skeletal muscle tissue development / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / canonical NF-kappaB signal transduction / transcription initiation-coupled chromatin remodeling / positive regulation of TORC1 signaling / Regulation of TP53 Activity through Acetylation / RORA activates gene expression / CD209 (DC-SIGN) signaling / negative regulation of autophagy / B cell differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / SUMOylation of transcription cofactors / regulation of signal transduction by p53 class mediator / regulation of autophagy / transcription coregulator binding
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone acetyltransferase p300
Similarity search - Component
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.
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
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  • Surface view colored by radius
  • Surface level: 0.024
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  • Surface view with fitted model
  • Atomic models: PDB-6k4n
  • Surface level: 0.024
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k4n
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6792.png

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)
AnnotationCryo-EM structure of p300. Transcriptional coactivator p300 is a large, multidomain protein that possess (HAT) histone acetyltransferase activity.
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
Components
  • Organelle or cellular component: p300 protein
    • Protein or peptide: Histone acetyltransferase p300

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Supramolecule #1: p300 protein

SupramoleculeName: p300 protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Histone acetyltransferase p300

MacromoleculeName: Histone acetyltransferase p300 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.100062 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KKIFKPEELR QALMPTLEAL YRQDPESLPF RQPVDPQLLG IPDYFDIVKS PMDLSTIKRK LDTGQYQEPW QYVDDIWLMF NNAWLYNRK TSRVYKYCSK LSEVFEQEID PVMQSLGYCC GRKLEFSPQT LCCYGKQLCT IPRDATYYSY QNRYHFCEKC F NEIQGESV ...String:
KKIFKPEELR QALMPTLEAL YRQDPESLPF RQPVDPQLLG IPDYFDIVKS PMDLSTIKRK LDTGQYQEPW QYVDDIWLMF NNAWLYNRK TSRVYKYCSK LSEVFEQEID PVMQSLGYCC GRKLEFSPQT LCCYGKQLCT IPRDATYYSY QNRYHFCEKC F NEIQGESV SLGDDPSQPQ TTINKEQFSK RKNDTLDPEL FVECTECGRK MHQICVLHHE IIWPAGFVCD GCLKKSARTR KE NKFSAKR LPSTRLGTFL ENRVNDFLRR QNHPESGEVT VRVVHASDKT VEVKPGMKAR FVDSGEMAES FPYRTKALFA FEE IDGVDL CFFGMHVQEY GSDCPPPNQR RVYISYLDSV HFFRPKCLRT AVYHEILIGY LEYVKKLGYT TGHIWACPPS EGDD YIFHC HPPDQKIPKP KRLQEWYKKM LDKAVSERIV HDYKDIFKQA TEDRLTSAKE LPYFEGDFWP NVLEESIKEL EQEEE ERKR EENTSNESTD VTKGDSKNAK KKNNKKTSKN KSSLSRGNKK KPGMPNVSND LSQKLYATME KHKEVFFVIR LIAGPA ANS LPPIVDPDPL IPCDLMDGRD AFLTLARDKH LEFSSLRRAQ WSTMCMLVEL HTQSQD

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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

BufferpH: 8
Component:
ConcentrationName
10.0 mMTris-Cl
150.0 mMNaClSodium chloride
1.0 mMDTT
2.0 mMPMSF
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 78894 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 15.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: EMAN2 (ver. 2.12), SPIDER)
Startup modelType of model: NONE / Details: Initial model was generated using EMAN2
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN2 (ver. 2.12)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 16152
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4bhw


Chain - Chain ID: A / Chain - Residue range: 1046-1664
Output model

PDB-6k4n:
Cryo-EM structure of p300

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