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- PDB-5u4k: NMR structure of the complex between the KIX domain of CBP and th... -

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Basic information

Entry
Database: PDB / ID: 5u4k
TitleNMR structure of the complex between the KIX domain of CBP and the transactivation domain 1 of p65
Components
  • CREB-binding protein
  • Transcription factor p65
KeywordsTRANSCRIPTION / p300-CBP coactivator family / NF-KB / transactivation domain
Function / homology
Function and homology information


Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex ...Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / Cytoprotection by HMOX1 / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / negative regulation of interferon-beta production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / histone H3K18 acetyltransferase activity / cellular response to interleukin-6 / Interleukin-1 processing / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / actinin binding / MRF binding / cellular response to angiotensin / response to UV-B / peroxisome proliferator activated receptor binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / face morphogenesis / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / peptide-lysine-N-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of dendritic spine development / positive regulation of miRNA metabolic process / response to cobalamin / positive regulation of T cell receptor signaling pathway / non-canonical NF-kappaB signal transduction / phosphate ion binding / SMAD binding / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / behavioral response to cocaine / acetyltransferase activity / The NLRP3 inflammasome / TFIIB-class transcription factor binding / general transcription initiation factor binding / positive regulation of double-strand break repair via homologous recombination / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / histone acetyltransferase complex / positive regulation of vascular endothelial growth factor production / neuropeptide signaling pathway / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / positive regulation of G1/S transition of mitotic cell cycle / cellular response to interleukin-1 / cellular defense response / long-term memory / Purinergic signaling in leishmaniasis infection / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / NF-kB is activated and signals survival
Similarity search - Function
Coactivator CBP, KIX domain / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain ...Coactivator CBP, KIX domain / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / 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 / Serum Albumin; Chain A, Domain 1 / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / ig-like, plexins, transcription factors / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / IPT domain / p53-like transcription factor, DNA-binding / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone lysine acetyltransferase CREBBP / Histone lysine acetyltransferase CREBBP / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLecoq, L. / Raiola, L. / Chabot, P.R. / Cyr, N. / Arseneault, G. / Omichinski, J.G.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-kappa B and transcription regulatory factors.
Authors: Lecoq, L. / Raiola, L. / Chabot, P.R. / Cyr, N. / Arseneault, G. / Legault, P. / Omichinski, J.G.
History
DepositionDec 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Feb 1, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Feb 8, 2023Group: Data collection / Refinement description
Category: pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_representative
Item: _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: Transcription factor p65


Theoretical massNumber of molelcules
Total (without water)13,7322
Polymers13,7322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1190 Å2
ΔGint-9 kcal/mol
Surface area7570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 260structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CREB-binding protein


Mass: 10353.856 Da / Num. of mol.: 1 / Fragment: KIX domain (UNP residues 25-111)
Source method: isolated from a genetically manipulated source
Details: KIX domain: residues 586-672. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1RPQ3, UniProt: P45481*PLUS
#2: Protein/peptide Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 3378.591 Da / Num. of mol.: 1 / Fragment: transactivation domain 1 (UNP residues 521-551)
Source method: isolated from a genetically manipulated source
Details: p65 transactivation domain 1, residues 532-551. / Source: (gene. exp.) Homo sapiens (human) / Gene: RELA, NFKB3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04206

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CB
141isotropic13D (H)CCH-TOCSY
151isotropic13D H(CCO)NH
162isotropic12D 1H-13C HSQC
1172isotropic13D 1H-13C NOESY
1163isotropic12D 1H-15N HSQC
1153isotropic13D HNCO
1143isotropic13D HN(CA)CB
1133isotropic13D (H)CCH-TOCSY
1123isotropic13D H(CCO)NH
1113isotropic13D 1H-15N NOESY
1104isotropic12D 1H-13C HSQC aliphatic
194isotropic12D 1H-13C HSQC aromatic
184isotropic13D 1H-13C NOESY
174isotropic23D-intermolecular-NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] p65 TA1, 2.4 mM KIX domain, 90% H2O/10% D2Op65 + 3eq KIX13C_15N_p65_KIX90% H2O/10% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] p65 TA1, 2.4 mM CBP-KIX, 100% D2Op65 + 3eq KIX in D2O13C_15N_p65_KIX_D2O100% D2O
solution30.8 mM [U-99% 13C; U-99% 15N] CBP-KIX, 2.4 mM p65 TA1, 90% H2O/10% D2OKIX + 3eq p6513C_15N_KIX_p6590% H2O/10% D2O
solution40.8 mM [U-99% 13C; U-99% 15N] CBP-KIX, 2.4 mM p65 TA1, 100% D2OKIX + 3eq p6513C_15N_KIX_p65_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMp65 TA1[U-99% 13C; U-99% 15N]1
2.4 mMKIX domainnatural abundance1
0.8 mMp65 TA1[U-99% 13C; U-99% 15N]2
2.4 mMCBP-KIXnatural abundance2
0.8 mMCBP-KIX[U-99% 13C; U-99% 15N]3
2.4 mMp65 TA1natural abundance3
0.8 mMCBP-KIX[U-99% 13C; U-99% 15N]4
2.4 mMp65 TA1natural abundance4
Sample conditionsIonic strength: 0 M / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYINOVAVarianUNITYINOVA6001
Varian UNITYINOVAVarianUNITYINOVA8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AnalysisCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 260 / Conformers submitted total number: 20

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