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- PDB-2lqh: NMR structure of FOXO3a transactivation domains (CR2C-CR3) in com... -

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Basic information

Entry
Database: PDB / ID: 2lqh
TitleNMR structure of FOXO3a transactivation domains (CR2C-CR3) in complex with CBP KIX domain (2b3l conformation)
Components
  • CREB-binding protein
  • Forkhead box O3
KeywordsTRANSCRIPTION / promiscuous binding / intrinsic disorder
Function / homology
Function and homology information


positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / 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 / Regulation of gene expression by Hypoxia-inducible Factor ...positive regulation of muscle atrophy / initiation of primordial ovarian follicle growth / positive regulation of hydrogen peroxide-mediated programmed cell death / 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 / Regulation of gene expression by Hypoxia-inducible Factor / 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 / cAMP response element binding protein binding / Notch-HLH transcription pathway / mitochondrial transcription factor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / RUNX3 regulates BCL2L11 (BIM) transcription / RNA polymerase II transcription repressor complex / FOXO-mediated transcription of cell cycle genes / cellular response to corticosterone stimulus / AKT phosphorylates targets in the nucleus / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / response to water-immersion restraint stress / neuronal stem cell population maintenance / ovulation from ovarian follicle / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / regulation of neural precursor cell proliferation / peptide lactyltransferase (CoA-dependent) activity / response to fatty acid / mitochondrial transcription / outer kinetochore / negative regulation of interferon-beta production / Signaling by NODAL / N-terminal peptidyl-lysine acetylation / brain morphogenesis / MRF binding / Regulation of FOXO transcriptional activity by acetylation / oocyte maturation / face morphogenesis / positive regulation of regulatory T cell differentiation / negative regulation of transcription by RNA polymerase I / antral ovarian follicle growth / protein-lysine-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / response to starvation / response to dexamethasone / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / acetyltransferase activity / histone H3K18 acetyltransferase activity / FOXO-mediated transcription of cell death genes / histone H3K27 acetyltransferase activity / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of reactive oxygen species biosynthetic process / histone acetyltransferase activity / TFIIB-class transcription factor binding / histone acetyltransferase complex / Regulation of localization of FOXO transcription factors / positive regulation of endothelial cell apoptotic process / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of neuron differentiation / canonical Wnt signaling pathway / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of double-strand break repair via homologous recombination / cellular response to glucose starvation / histone acetyltransferase / positive regulation of DNA-binding transcription factor activity / tumor necrosis factor-mediated signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of autophagy / FLT3 Signaling / negative regulation of cell migration / positive regulation of erythrocyte differentiation / transcription coregulator binding / MAPK6/MAPK4 signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA damage response, signal transduction by p53 class mediator / cellular response to glucose stimulus / chromatin DNA binding / negative regulation of canonical Wnt signaling pathway / cellular response to nerve growth factor stimulus / protein destabilization / PML body / beta-catenin binding / cellular response to virus / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / sequence-specific double-stranded DNA binding / disordered domain specific binding / cellular response to UV / rhythmic process
Similarity search - Function
FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / Coactivator CBP, KIX domain / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / Coactivator CBP, KIX domain / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / 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 / Serum Albumin; Chain A, Domain 1 / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Forkhead box protein O3 / Histone lysine acetyltransferase CREBBP
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, F. / Marshall, C.B. / Yamamoto, K. / Li, G.B. / Gasmi-Seabrook, G.M.C. / Okada, H. / Mak, T.W. / Ikura, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structures of KIX domain of CBP in complex with two FOXO3a transactivation domains reveal promiscuity and plasticity in coactivator recruitment.
Authors: Wang, F. / Marshall, C.B. / Yamamoto, K. / Li, G.Y. / Gasmi-Seabrook, G.M. / Okada, H. / Mak, T.W. / Ikura, M.
History
DepositionMar 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: 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_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: Forkhead box O3


Theoretical massNumber of molelcules
Total (without water)15,5622
Polymers15,5622
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 / 100structures 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Production host: Escherichia coli (E. coli) / References: UniProt: P45481, histone acetyltransferase
#2: Protein Forkhead box O3 / FOXO3a


Mass: 5208.519 Da / Num. of mol.: 1 / Fragment: Transactivation domains (CR2C-CR3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O43524*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D 1H-15N NOESY
1622D 1H-13C HSQC
1723D (H)CCH-TOCSY
1823D 1H-13C NOESY
1932D 1H-15N HSQC
11033D HNCO
11133D HN(CA)CB
11233D CBCA(CO)NH
11333D 1H-15N NOESY
11442D 1H-13C HSQC
11543D (H)CCH-TOCSY
11643D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] KIX, 0.6 mM CR2C-CR3, 20 mM MES, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 13C; U-100% 15N] KIX, 0.6 mM CR2C-CR3, 20 mM MES, 50 mM sodium chloride, 1 mM DTT, 100% D2O100% D2O
30.6 mM [U-100% 13C; U-100% 15N] CR2C-CR3, 0.6 mM KIX, 20 mM MES, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
40.6 mM [U-100% 13C; U-100% 15N] CR2C-CR3, 0.6 mM KIX, 20 mM MES, 50 mM sodium chloride, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMKIX-1[U-100% 13C; U-100% 15N]1
0.6 mMCR2C-CR3-21
20 mMMES-31
50 mMsodium chloride-41
1 mMDTT-51
0.6 mMKIX-6[U-100% 13C; U-100% 15N]2
0.6 mMCR2C-CR3-72
20 mMMES-82
50 mMsodium chloride-92
1 mMDTT-102
0.6 mMCR2C-CR3-11[U-100% 13C; U-100% 15N]3
0.6 mMKIX-123
20 mMMES-133
50 mMsodium chloride-143
1 mMDTT-153
0.6 mMCR2C-CR3-16[U-100% 13C; U-100% 15N]4
0.6 mMKIX-174
20 mMMES-184
50 mMsodium chloride-194
1 mMDTT-204
Sample conditionsIonic strength: 0.05 / pH: 6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: RECOORD water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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