[English] 日本語
Yorodumi
- PDB-5xzc: Cryo-EM structure of p300-p53 protein complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5xzc
TitleCryo-EM structure of p300-p53 protein complex
Components
  • Cellular tumor antigen p53P53
  • Histone acetyltransferase p300
KeywordsTRANSCRIPTION / transcription factor / autoacetylation / allosteric interaction / catalytically active form
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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single 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, N.S. / Sengupta, J. / Roy, S. / Kundu, T.K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 12, 2017 / Release: Jan 23, 2019

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6791
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6791
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone acetyltransferase p300
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
E: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)191,6965
Polyers191,6965
Non-polymers00
Water0
1
A: Histone acetyltransferase p300


Theoretical massNumber of molelcules
Total (without water)72,1001
Polyers72,1001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
E: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)119,5964
Polyers119,5964
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
DetailsOne molecule of p300 interacts with four molecules of p53 (i.e, p300 monomer interacts with p53 tetramer)

-
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
#2: Protein/peptide
Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53 / Coordinate model: Cα atoms only


Mass: 29898.908 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: p300-p53 complex / Type: COMPLEX
Details: Proteins were purified separately and then complex was made for cryo-EM.
Entity ID: 1, 2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
110 mMTris-Cl1
2150 mMNacl1
35 mMMgCl21
420 microMZnCl21
52 mMPMSF1
61 mMDTT1
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

-
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: 1700 nm / Calibrated defocus min: 1700 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)

-
Processing

EM software
IDNameVersionCategoryDetailsFitting ID
1EMAN22.12particle selectionparticles picked semiautomatically: using both e2boxer.py and manually.
2SPIDERparticle selectionparticles picked in EMAN2 and exported to SPIDER and also particles were picked separately in SPIDER
3TIA4.7image acquisition
5EMAN22.12CTF correction
6SPIDERCTF correction
9UCSF Chimera1.11model fittingCrystal structure 4BHW fitted using Chimera. The bromodomain matches remarkably well with the central spout. RING and PHD domains are fitted manually at the weak densities beside the bromodomain.1
12PyMOLmodel fittingp53 dimers (pdb: 3KMD) fitted manually in both the side-lobes of p53 density.2
14EMAN22.12initial Euler assignment
15SPIDERfinal Euler assignment
16SPIDERclassification
17SPIDER3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 10.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10088 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model building
ID
1
2
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range
14BHW

4bhw

A11046-1664
23KMD

3kmd

292-291
31C26

1c26

2325-356
Least-squares processHighest resolution: 10.7 Å

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more