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- PDB-2ka4: NMR structure of the CBP-TAZ1/STAT2-TAD complex -

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Basic information

Entry
Database: PDB / ID: 2ka4
TitleNMR structure of the CBP-TAZ1/STAT2-TAD complex
Components
  • Crebbp protein
  • Signal transducer and activator of transcription 2
KeywordsTranscription regulator / CBP/p300 / STAT2 / TAZ1 / transactivation domain / Bromodomain / Activator / Alternative splicing / Antiviral defense / Cytoplasm / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Polymorphism / SH2 domain / Transcription / Transcription regulation
Function / homology
Function and homology information


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 / 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 ...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 / 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / negative regulation of interferon-beta production / N-terminal peptidyl-lysine acetylation / MRF binding / face morphogenesis / Interleukin-20 family signaling / negative regulation of transcription by RNA polymerase I / negative regulation of type I interferon-mediated signaling pathway / protein-lysine-acetyltransferase activity / type I interferon-mediated signaling pathway / cellular response to hepatocyte growth factor stimulus / regulation of mitochondrial fission / histone acetyltransferase activity / acetyltransferase activity / ubiquitin-like protein ligase binding / Regulation of IFNA/IFNB signaling / regulation of protein phosphorylation / TFIIB-class transcription factor binding / histone acetyltransferase complex / cell surface receptor signaling pathway via JAK-STAT / positive regulation of double-strand break repair via homologous recombination / 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 / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of DNA-binding transcription factor activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / defense response / protein destabilization / PML body / Evasion by RSV of host interferon responses / cellular response to virus / response to peptide hormone / RNA polymerase II transcription regulator complex / disordered domain specific binding / Interferon alpha/beta signaling / cellular response to UV / rhythmic process / regulation of cell population proliferation / DNA-binding transcription factor binding / molecular adaptor activity / defense response to virus / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / damaged DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding
Similarity search - Function
Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / CREB-binding Protein; Chain A / TAZ domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : ...Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / CREB-binding Protein; Chain A / TAZ 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 transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker 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 / : / 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. / p53-like transcription factor, DNA-binding / Nuclear receptor coactivator, interlocking / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / 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
Similarity search - Domain/homology
Histone lysine acetyltransferase CREBBP / Signal transducer and activator of transcription 2 / histone acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsWojciak, J.M. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
CitationJournal: 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
DepositionOct 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.4May 8, 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: Crebbp protein
B: Signal transducer and activator of transcription 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9085
Polymers17,7112
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Crebbp protein


Mass: 11281.177 Da / Num. of mol.: 1 / Fragment: UNP residues 340 to 439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species: musculus / Gene: Crebbp / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GQV9, UniProt: P45481*PLUS
#2: Protein Signal transducer and activator of transcription 2 / p113


Mass: 6430.196 Da / Num. of mol.: 1 / Fragment: UNP residues 786 to 838
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: STAT2 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: P52630
#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 experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 15N] ALANINE, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: ALANINE / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 0.05 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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