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- PDB-1jsp: NMR Structure of CBP Bromodomain in complex with p53 peptide -

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Entry
Database: PDB / ID: 1jsp
TitleNMR Structure of CBP Bromodomain in complex with p53 peptide
Components
  • CREB-BINDING PROTEIN
  • tumor protein p53
KeywordsDNA BINDING PROTEIN / Bromodomain / CBP / NMR structure.
Function / homology
Function and homology information


protein N-acetyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes ...protein N-acetyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / mRNA transcription / positive regulation of programmed necrotic cell death / RUNX3 regulates NOTCH signaling / bone marrow development / circadian behavior / T cell proliferation involved in immune response / NOTCH4 Intracellular Domain Regulates Transcription / Nuclear events mediated by NFE2L2 / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / Regulation of NFE2L2 gene expression / RUNX3 regulates CDKN1A transcription / Regulation of gene expression by Hypoxia-inducible Factor / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of transcription by RNA polymerase I / TRAF6 mediated IRF7 activation / histone deacetylase regulator activity / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / protein-lysine-acetyltransferase activity / negative regulation of neuroblast proliferation / T cell lineage commitment / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / mitochondrial DNA repair / histone H3K4 acetyltransferase activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein acetylation / ER overload response / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / homeostatic process / thymocyte apoptotic process / B cell lineage commitment / Notch-HLH transcription pathway / histone H4K12 acetyltransferase activity / TP53 Regulates Transcription of Caspase Activators and Caspases / histone H3K14 acetyltransferase activity / negative regulation of mitophagy / histone H4K16 acetyltransferase activity / cardiac septum morphogenesis / Formation of paraxial mesoderm / histone H3K9 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K122 acetyltransferase activity / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / FOXO-mediated transcription of cell death genes / PI5P Regulates TP53 Acetylation / stimulatory C-type lectin receptor signaling pathway / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA)
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 / : / Histone acetyltransferase p300-like, PHD 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 / : / Histone acetyltransferase p300-like, PHD domain / 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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / Zinc finger ZZ-type signature. / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / 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. / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain (BrD) profile. / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellular tumor antigen p53 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsHe, Y. / Mujtaba, S. / Zeng, L. / Yan, S. / Zhou, M.-M.
CitationJournal: Mol.Cell / Year: 2004
Title: Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation.
Authors: Mujtaba, S. / He, Y. / Zeng, L. / Yan, S. / Plotnikova, O. / Sachchidanand / Sanchez, R. / Zeleznik-Le, N.J. / Ronai, Z. / Zhou, M.M.
History
DepositionAug 17, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: tumor protein p53
B: CREB-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,8252
Polymers16,8252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein/peptide tumor protein p53


Mass: 2406.891 Da / Num. of mol.: 1 / Fragment: C-terminal fragment / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P04637
#2: Protein CREB-BINDING PROTEIN / CBP


Mass: 14418.547 Da / Num. of mol.: 1 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92793
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N-HSQC
4243D CBCA(CO)NH
3333D (H)CCH-TOCSY
3433D 13C-edited 13C/15N-filtered NOESY
1513D 15N-separated NOESY
2623D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM CBP bromodomain U-15N; 0.5mM P53 peptide; 100mM phosphate buffer; pH 6.590% H2O/10% D2O
20.5mM CBP bromodomain U-15N,13C; 0.5mM P53 peptide;100mM phosphate buffer; pH 6.590% H2O/10% D2O
30.5mM CBP bromodomain U-15N,13C; 0.5mM P53 peptide;100mM phosphate buffer; pH 6.599.9%D2O
40.5mM CBP bromodomain U-15N,13C,75% 2H; 0.5mM P53 peptide;100mM phosphate buffer; pH 6.590% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5ambient 298 K
26.5ambient 298 K
36.5ambient 298 K
46.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Frank Delaglioprocessing
NMRView5.0.3Bruce Johnsondata analysis
X-PLOR3.1Axel Brungerstructure solution
ARIA0.1Michael Nilgesiterative matrix relaxation
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: 71 inter-molecular NOEs are observed between protein and peptide.
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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