PDB-2ka6: NMR structure of the CBP-TAZ2/STAT1-TAD complex

Basic information

• Entry: Database: PDB / ID: 2ka6
• Title: NMR structure of the CBP-TAZ2/STAT1-TAD complex

Components

• CREB-binding protein
• Signal transducer and activator of transcription 1-alpha/beta

• Keywords: TRANSCRIPTION REGULATOR / CBP/p300 / TAZ2 / STAT1 / transactivation domain / Bromodomain / Activator / Alternative splicing / Antiviral defense / Cytoplasm / Disease mutation / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Polymorphism / SH2 domain / Transcription / Transcription regulation / Acetylation / Chromosomal rearrangement / Metal-binding / Methylation / Transferase / Ubl conjugation / Zinc / Zinc-finger

Function / homology

Function:

metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 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 / response to interferon-beta / Attenuation phase / metanephric mesenchymal cell proliferation involved in metanephros 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 / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / CCR5 chemokine receptor binding / Regulation of lipid metabolism by PPARalpha / negative regulation of viral process / Interleukin-9 signaling / Interleukin-21 signaling / Cytoprotection by HMOX1 / interleukin-9-mediated signaling pathway / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / outer kinetochore / negative regulation of interferon-beta production / histone H3K27 acetyltransferase activity / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / MRF binding / tumor necrosis factor receptor binding / Signaling by cytosolic FGFR1 fusion mutants / blood circulation / peroxisome proliferator activated receptor binding / Interleukin-35 Signalling / Interleukin-27 signaling / face morphogenesis / negative regulation of transcription by RNA polymerase I / positive regulation of dendritic spine development / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of mesenchymal cell proliferation / histone acetyltransferase binding / peptide-lysine-N-acetyltransferase activity / macrophage derived foam cell differentiation / cellular response to hepatocyte growth factor stimulus / Interleukin-20 family signaling / negative regulation of endothelial cell proliferation / Interleukin-6 signaling / type I interferon-mediated signaling pathway / response to type II interferon / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / ubiquitin-like protein ligase binding / positive regulation of nitric-oxide synthase biosynthetic process / behavioral response to cocaine / non-canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / acetyltransferase activity / cellular response to nutrient levels / cell surface receptor signaling pathway via JAK-STAT / TFIIB-class transcription factor binding / cellular response to organic cyclic compound / histone acetyltransferase complex / Regulation of IFNA/IFNB signaling / positive regulation of G1/S transition of mitotic cell cycle / long-term memory / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interferon-beta / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / response to mechanical stimulus / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / negative regulation of canonical NF-kappaB signal transduction / Growth hormone receptor signaling / histone acetyltransferase activity / Signaling by CSF3 (G-CSF) / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of defense response to virus by host / response to cAMP / tumor necrosis factor-mediated signaling pathway / Downstream signal transduction / negative regulation of angiogenesis / response to nutrient / transcription corepressor binding / positive regulation of erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / protein phosphatase 2A binding / response to cytokine / promoter-specific chromatin binding

Domain/homology:

signal transducer and activator of transcription 1 / Signal transducer and activation of transcription 1, TAZ2 binding domain, C-terminal / STAT1, SH2 domain / STAT1, C-terminal domain superfamily / STAT1 TAZ2 binding domain / CREB-binding Protein; Chain A / TAZ domain / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / 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 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / p53-like transcription factor, DNA-binding / Nuclear receptor coactivator, interlocking / Helix non-globular / SH2 domain / Special / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha

Component:

Signal transducer and activator of transcription 1-alpha/beta / Histone lysine acetyltransferase CREBBP

• Biological species: Mus musculus (house mouse); Homo sapiens (human)
• Method: SOLUTION NMR / molecular dynamics
• Authors: Wojciak, J.M. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
• Citation: Journal: Embo J. / Year: 2009; Title: Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains.; Authors: Wojciak, J.M. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.

History

Deposition	Oct 30, 2008	Deposition site: BMRB / Processing site: RCSB
Revision 1.0	Apr 7, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 19, 2020	Group: Data collection / Database references / Derived calculations / Other Category: database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: CREB-binding protein

B: Signal transducer and activator of transcription 1-alpha/beta

hetero molecules

Summary:

• 15.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	15,765	5
Polymers	15,569	2
Non-polymers	196	3
Water	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555		1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	20 / 200	structures with the lowest energy
Representative	Model #1	closest to the average

Components

#1: Protein

A CREB-binding protein /

Details:

Mass: 10527.567 Da / Num. of mol.: 1 / Fragment: UNP residues 1764 to 1855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbp, Crebbp / Production host: Escherichia coli (E. coli) / References: UniProt: P45481, histone acetyltransferase

#2: Protein/peptide

B Signal transducer and activator of transcription 1-alpha/beta / Transcription factor ISGF-3 components p91/p84

Details:

Mass: 5041.582 Da / Num. of mol.: 1 / Fragment: UNP residues 710 to 750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P42224

#3: Chemical

A-93 A-94 A-95 ChemComp-ZN / ZINC ION

Details:

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

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR
• NMR experiment: Type: 2D 1H-15N HSQC

Sample preparation

• Details: Contents: 1 mM [U-100% 15N] TAZ2, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
• Sample: Conc.: 1 mM / Component: TAZ2 / Isotopic labeling: [U-100% 15N]
• Sample conditions: Ionic strength: 0.05 / pH: 6.8 / Pressure: ambient / Temperature: 290 K

NMR measurement

NMR spectrometer

Type	Manufacturer	Model	Field strength (MHz)	Spectrometer-ID
Bruker DRX	Bruker	DRX	600	1
Bruker Avance	Bruker	AVANCE	900	2

Processing

• NMR software: Name: Amber; Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm; Classification: refinement
• Refinement: Method: molecular dynamics / Software ordinal: 1
• NMR representative: Selection criteria: closest to the average
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 200 / Conformers submitted total number: 20