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- PDB-1kdx: KIX DOMAIN OF MOUSE CBP (CREB BINDING PROTEIN) IN COMPLEX WITH PH... -

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Basic information

Entry
Database: PDB / ID: 1kdx
TitleKIX DOMAIN OF MOUSE CBP (CREB BINDING PROTEIN) IN COMPLEX WITH PHOSPHORYLATED KINASE INDUCIBLE DOMAIN (PKID) OF RAT CREB (CYCLIC AMP RESPONSE ELEMENT BINDING PROTEIN), NMR 17 STRUCTURES
Components
  • CBP
  • CREB
KeywordsTRANSCRIPTION REGULATION COMPLEX / COMPLEX (TRANSCRIPTION ACTIVATOR-CO-ACTIVATOR) / PROTEIN-PROTEIN INTERACTION / PHOSPHOSERINE RECOGNITION
Function / homology
Function and homology information


CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / NGF-stimulated transcription / chemotaxis to arachidonic acid / AKT phosphorylates targets in the nucleus / transcription coactivator binding => GO:0001223 / ATF4-CREB1 transcription factor complex / euchromatin => GO:0000791 / positive regulation of transforming growth factor beta3 production / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 ...CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / NGF-stimulated transcription / chemotaxis to arachidonic acid / AKT phosphorylates targets in the nucleus / transcription coactivator binding => GO:0001223 / ATF4-CREB1 transcription factor complex / euchromatin => GO:0000791 / positive regulation of transforming growth factor beta3 production / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / cAMP response element binding / secretory granule organization / : / lung saccule development / positive regulation of cardiac muscle tissue development / 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 / regulation of glial cell proliferation / Attenuation phase / lung epithelium development / 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 / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / NCAM signaling for neurite out-growth / : / regulation of fibroblast proliferation / pituitary gland development / positive regulation of cell adhesion molecule production / response to xenobiotic stimulus => GO:0009410 / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / chromatin => GO:0000785 / Cytoprotection by HMOX1 / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / negative regulation of transcription by competitive promoter binding / positive regulation of hormone secretion / mammary gland development / negative regulation of interferon-beta production / positive regulation of multicellular organism growth / arrestin family protein binding / histone H3K18 acetyltransferase activity / positive regulation of osteoclast differentiation / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / MRF binding / peroxisome proliferator activated receptor binding / response to glucagon / face morphogenesis / negative regulation of transcription by RNA polymerase I / cellular response to zinc ion / cellular response to insulin-like growth factor stimulus / cellular response to fatty acid / response to L-glutamate / peptide-lysine-N-acetyltransferase activity / regulation of cell size / histone acetyltransferase binding / type I pneumocyte differentiation / cellular response to hepatocyte growth factor stimulus / positive regulation of dendritic spine development / cellular response to platelet-derived growth factor stimulus / SMAD binding / behavioral response to cocaine / transcription factor binding / acetyltransferase activity / TFIIB-class transcription factor binding / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / positive regulation of fat cell differentiation / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of RNA polymerase II transcription preinitiation complex assembly / long-term memory / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to transforming growth factor beta stimulus / Hsp70 protein binding / lactation / axonogenesis / transforming growth factor beta receptor signaling pathway / : / cellular response to nerve growth factor stimulus / response to activity / cellular response to leukemia inhibitory factor / positive regulation of long-term synaptic potentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding
Similarity search - Function
cAMP-responsive element-binding protein 1 / cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / Coactivator CBP, KIX domain / bZIP transcription factor / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding ...cAMP-responsive element-binding protein 1 / cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / Coactivator CBP, KIX domain / bZIP transcription factor / 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. / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / basic region leucin zipper / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Serum Albumin; Chain A, Domain 1 / Basic-leucine zipper domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclic AMP-responsive element-binding protein 1 / Histone lysine acetyltransferase CREBBP
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / DG, SA
AuthorsRadhakrishnan, I. / Perez-Alvarado, G.C. / Dyson, H.J. / Wright, P.E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator:coactivator interactions.
Authors: Radhakrishnan, I. / Perez-Alvarado, G.C. / Parker, D. / Dyson, H.J. / Montminy, M.R. / Wright, P.E.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBP
B: CREB


Theoretical massNumber of molelcules
Total (without water)12,9432
Polymers12,9432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 40LOWEST CONSTRAINT ENERGIES
RepresentativeModel #1

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Components

#1: Protein CBP / CREB-BINDING PROTEIN


Mass: 9552.860 Da / Num. of mol.: 1 / Fragment: KIX, RESIDUES 586-666
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED AT SER 133 / Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Plasmid: PET21A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P45481
#2: Protein/peptide CREB / CAMP-RESPONSE ELEMENT BINDING PROTEIN / CREB


Mass: 3389.695 Da / Num. of mol.: 1 / Fragment: KID, RESIDUES 101-160
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED AT SER 133 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PET24A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15337

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE-RESONANCE EXPERIMENTS: HNCA
121HN(CO)CA
131CBCA(CO)NH
141HN(CA)CB; DOUBLE-RESONANCE: 15N-EDITED TOCSY
151(H)CCH-TOCSY
161(H)CCH-COSY; FOR RESTRAINT GENERATION: 15N- AND 13C-EDITED NOESYS
171SELECT-FILTERED NOESY
181DOUBLE HALF-FILTERED NOESY
191HNHA
1101CONSTANT-TIME SPIN-ECHO DIFFERENCE EXPERIMENTS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING RESTRAINTS DERIVED FROM 15N- AND 13C-EDITED NOESYS, SELECT-FILTERED NOESY, DOUBLE HALF-FILTERED NOESY, HNHA AND CONSTANT TIME SPIN-ECHO-DIFFERENCE EXPERIMENTS.

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Sample preparation

DetailsContents: H2O OR D2O
Sample conditionsIonic strength: 0.07 / pH: 5.5 / Pressure: 1 atm / Temperature: 315 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX7503

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
DIANAWUTHRICH PROGRAM 2 : AMBER 4.1 AUTHORS 2 : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
MSI FELIX95FELIX95structure solution
RefinementMethod: DG, SA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST CONSTRAINT ENERGIES / Conformers calculated total number: 40 / Conformers submitted total number: 17

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