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- PDB-2c52: Structural diversity in CBP p160 complexes -

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Basic information

Entry
Database: PDB / ID: 2c52
TitleStructural diversity in CBP p160 complexes
Components
  • CREB-BINDING PROTEIN
  • NUCLEAR RECEPTOR COACTIVATOR 1
KeywordsTRANSFERASE / ACTIVATOR / BROMODOMAIN / METAL-BINDING / METHYLATION / NUCLEAR PROTEIN / TRANSCRIPTION / TRANSCRIPTION REGULATION / ZINC / ZINC-FINGER / ACYLTRANSFERASE / ALTERNATIVE SPLICING / CHROMOSOMAL TRANSLOCATION / POLYMORPHISM / PROTO-ONCOGENE / UBL CONJUGATION
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 / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling ...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 / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / cAMP response element binding protein binding / Notch-HLH transcription pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / protein K48-linked deubiquitination / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / negative regulation of interferon-beta production / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / MRF binding / positive regulation of female receptivity / peroxisome proliferator activated receptor binding / face morphogenesis / negative regulation of transcription by RNA polymerase I / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to hepatocyte growth factor stimulus / acetyltransferase activity / histone acetyltransferase activity / male mating behavior / hypothalamus development / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of dendritic spine development / TFIIB-class transcription factor binding / progesterone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / histone acetyltransferase complex / : / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / protein-lysine-acetyltransferase activity / estrous cycle / positive regulation of G1/S transition of mitotic cell cycle / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / long-term memory / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of double-strand break repair via homologous recombination / cellular response to hormone stimulus / estrogen receptor signaling pathway / energy homeostasis / Regulation of lipid metabolism by PPARalpha / lactation / behavioral response to cocaine / canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / response to progesterone / positive regulation of adipose tissue development / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of neuron differentiation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / SUMOylation of transcription cofactors / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / cellular response to nutrient levels / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / cellular response to virus / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of non-canonical NF-kappaB signal transduction / cerebral cortex development / PML body / mRNA transcription by RNA polymerase II
Similarity search - Function
Helix Hairpins - #410 / Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking 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. ...Helix Hairpins - #410 / Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking 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 / Nuclear receptor coactivator 1 / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Helix Hairpins / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Helix non-globular / PAS domain superfamily / Special / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone lysine acetyltransferase CREBBP / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodSOLUTION NMR / CANDID
AuthorsWaters, L.C. / Yue, B. / Veverka, V. / Renshaw, P.S. / Bramham, J. / Matsuda, S. / Frenkiel, T. / Kelly, G. / Muskett, F.W. / Carr, M.D. / Heery, D.M.
CitationJournal: J. Biol. Chem. / Year: 2006
Title: Structural diversity in p160/CREB-binding protein coactivator complexes.
Authors: Waters, L. / Yue, B. / Veverka, V. / Renshaw, P. / Bramham, J. / Matsuda, S. / Frenkiel, T. / Kelly, G. / Muskett, F. / Carr, M. / Heery, D.M.
History
DepositionOct 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-BINDING PROTEIN
B: NUCLEAR RECEPTOR COACTIVATOR 1


Theoretical massNumber of molelcules
Total (without water)12,8682
Polymers12,8682
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)37 / -
RepresentativeModel #20

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Components

#1: Protein CREB-BINDING PROTEIN


Mass: 6568.562 Da / Num. of mol.: 1 / Fragment: SID, RESIDUES 2059-2117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P45481, histone acetyltransferase
#2: Protein NUCLEAR RECEPTOR COACTIVATOR 1 / STEROID RECEPTOR COACTIVATOR 1 / NCOA-1 / SRC-1 / RIP160 / HIN-2 PROTEIN


Mass: 6299.123 Da / Num. of mol.: 1 / Fragment: AD1, RESIDUES 920-970
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q15788, histone acetyltransferase
Compound detailsACETYLATES HISTONES, GIVING A SPECIFIC TAG FOR TRANSCRIPTIONAL ACTIVATION AND NUCLEAR RECEPTOR ...ACETYLATES HISTONES, GIVING A SPECIFIC TAG FOR TRANSCRIPTIONAL ACTIVATION AND NUCLEAR RECEPTOR COACTIVATOR THAT DIRECTLY BINDS NUCLEAR RECEPTORS AND STIMULATES THE TRANSCRIPTIONAL ACTIVITIES

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-1H HSQC 15N-13C-1H HN(CA)CB 15N-13C-1H CBCA(CO)NH 15N-1H TOCSY-HSQC
22215N-1H NOESYHSQC
33313C-1H HMQCNOESY
44413C-1H HCCHTOCSY NOESY TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CBP-SID SRC1-AD1.

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Sample preparation

Details
Solution-IDContents
190% WATER/10% D2O
290% WATER/10% D2O
3100% D2O
4100% D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
1100 mM7298.0 K
2100 mM7298.0 K
3100 mM7298.0 K
4100 mM7298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA8003
Bruker AVANCEBrukerAVANCE6004

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT,MUMENTHALER,WUTHRICHrefinement
CYANAstructure solution
RefinementMethod: CANDID / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers submitted total number: 37

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