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- PDB-1r8u: NMR structure of CBP TAZ1/CITED2 complex -

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Basic information

Entry
Database: PDB / ID: 1r8u
TitleNMR structure of CBP TAZ1/CITED2 complex
Components
  • CREB-binding protein
  • Cbp/p300-interacting transactivator 2
KeywordsTRANSCRIPTION/TRANSCRIPTION ACTIVATOR / zinc-binding motifs / protein-protein complex / TAZ zinc finger / TRANSCRIPTION-TRANSCRIPTION ACTIVATOR COMPLEX
Function / homology
Function and homology information


embryonic process involved in female pregnancy / cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / left/right pattern formation / pulmonary artery morphogenesis / embryonic heart tube left/right pattern formation / regulation of animal organ formation / adrenal cortex formation / nodal signaling pathway / Activation of the TFAP2 (AP-2) family of transcription factors ...embryonic process involved in female pregnancy / cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / left/right pattern formation / pulmonary artery morphogenesis / embryonic heart tube left/right pattern formation / regulation of animal organ formation / adrenal cortex formation / nodal signaling pathway / 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 / embryonic camera-type eye morphogenesis / 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 / sex determination / Notch-HLH transcription pathway / positive regulation of male gonad development / Transcriptional and post-translational regulation of MITF-M expression and activity / endocardial cushion development / determination of left/right asymmetry in lateral mesoderm / positive regulation of peroxisome proliferator activated receptor signaling pathway / lens morphogenesis in camera-type eye / granulocyte differentiation / left/right axis specification / positive regulation of cell-cell adhesion / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / negative regulation of cardiac muscle cell proliferation / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / trophectodermal cell differentiation / peptide lactyltransferase (CoA-dependent) activity / response to fluid shear stress / outer kinetochore / peripheral nervous system development / negative regulation of interferon-beta production / Activation of the TFAP2 (AP-2) family of transcription factors / cardiac neural crest cell development involved in heart development / N-terminal peptidyl-lysine acetylation / MRF binding / bone morphogenesis / determination of left/right symmetry / face morphogenesis / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of transcription by RNA polymerase I / protein-lysine-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / ventricular septum morphogenesis / histone acetyltransferase binding / LBD domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / acetyltransferase activity / histone acetyltransferase activity / FOXO-mediated transcription of cell death genes / uterus development / heart looping / skeletal muscle cell differentiation / outflow tract morphogenesis / TFIIB-class transcription factor binding / decidualization / histone acetyltransferase complex / embryonic placenta development / erythrocyte development / positive regulation of double-strand break repair via homologous recombination / hematopoietic progenitor cell differentiation / vasculogenesis / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / response to mechanical stimulus / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / spleen development / positive regulation of cell cycle / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transforming growth factor beta receptor signaling pathway
Similarity search - Function
Helix Hairpins - #2200 / CITED / CITED / CREB-binding Protein; Chain A / TAZ 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 ...Helix Hairpins - #2200 / CITED / CITED / CREB-binding Protein; Chain A / TAZ 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 / 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. / Helix Hairpins / Nuclear receptor coactivator, interlocking / Helix non-globular / Special / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain (BrD) profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Histone lysine acetyltransferase CREBBP / Cbp/p300-interacting transactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / AMBER simulated annealing, minimization
AuthorsDe Guzman, R.N. / Martinez-Yamout, M. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Interaction of the TAZ1 domain of the CREB-binding protein with the activation domain of CITED2: regulation by competition between intrinsically unstructured ligands for non-identical binding sites.
Authors: De Guzman, R.N. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: Cbp/p300-interacting transactivator 2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3755
Polymers17,1792
Non-polymers1963
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 / 50structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cbp/p300-interacting transactivator 2 / MSG-related protein 1 / MRG1 protein / P35srj / CITED2


Mass: 5897.726 Da / Num. of mol.: 1 / Fragment: CITED2 CAD (residues 200-269)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CITED2, MRG1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99967
#2: Protein CREB-binding protein / CBP


Mass: 11281.177 Da / Num. of mol.: 1 / Fragment: CBP TAZ1 (residues 334-433)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 19547885, UniProt: P45481*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 15N-separated NOESY
3333D 13C-separated NOESY
4443D 13C-separated ROESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM N15 TAZ1, unlabeled CITED2, 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM unlabeled TAZ1, N15 CITED2, 90% H2O, 10% D2O90% H2O/10% D2O
30.5mM C13,N15 TAZ1, unlabeled CITED2, 90% H2O, 10% D2O90% H2O/10% D2O
40.5mM unlabeled TAZ1, CITED2, 90% H2O,10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
116 mM 6.81 atm298 K
216 mM 6.81 atm298 K
316 mM 6.81 atm298 K
416 mM 6.81 atm298 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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2003DeLaglio, Baxprocessing
NMRDraw4.1.3.Bruce Johnsondata analysis
DYANA1.5Peter Guntert et al.structure solution
Amber7David Case et al.refinement
RefinementMethod: AMBER simulated annealing, minimization / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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