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- PDB-1kbh: Mutual Synergistic Folding in the Interaction Between Nuclear Rec... -

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Basic information

Entry
Database: PDB / ID: 1kbh
TitleMutual Synergistic Folding in the Interaction Between Nuclear Receptor Coactivators CBP and ACTR
Components
  • CREB-BINDING PROTEIN
  • nuclear receptor coactivator
KeywordsTRANSCRIPTION / Nuclear Hormone Receptors / p160 / ACTR / CBP / CREB-binding protein / p300 / coactivator
Function / homology
Function and homology information


receptor transactivation / 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 / cell dedifferentiation / Attenuation phase / regulation of stem cell division / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...receptor transactivation / 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 / cell dedifferentiation / Attenuation phase / regulation of stem cell division / 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 / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / Regulation of lipid metabolism by PPARalpha / negative regulation of viral process / Cytoprotection by HMOX1 / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / outer kinetochore / negative regulation of interferon-beta production / positive regulation of keratinocyte differentiation / histone H3K27 acetyltransferase activity / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / MRF binding / peroxisome proliferator activated receptor binding / face morphogenesis / negative regulation of transcription by RNA polymerase I / nuclear thyroid hormone receptor binding / positive regulation of dendritic spine development / peptide-lysine-N-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / positive regulation of stem cell population maintenance / RNA polymerase II complex binding / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / behavioral response to cocaine / non-canonical NF-kappaB signal transduction / acetyltransferase activity / cellular response to nutrient levels / TFIIB-class transcription factor binding / histone acetyltransferase complex / positive regulation of G1/S transition of mitotic cell cycle / long-term memory / histone acetyltransferase activity / histone acetyltransferase / cellular response to hormone stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nuclear receptor coactivator activity / cellular response to estradiol stimulus / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / MAPK6/MAPK4 signaling / protein modification process / protein destabilization / transcription coactivator binding / PML body / PPARA activates gene expression / chromatin DNA binding / cellular response to virus / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein localization to nucleus / RNA polymerase II transcription regulator complex / transcription corepressor activity / cellular response to UV / rhythmic process / positive regulation of DNA-binding transcription factor activity / disordered domain specific binding / p53 binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / protein dimerization activity / molecular adaptor activity / nuclear body / protein domain specific binding / chromatin binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor coactivator, Ncoa-type, interlocking domain / Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking 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. ...Nuclear receptor coactivator, Ncoa-type, interlocking domain / Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking 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 / 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. / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Helix Hairpins / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Helix non-globular / Special / 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
Histone lysine acetyltransferase CREBBP / Nuclear receptor coactivator 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / Dyana, Sane, Amber
AuthorsDemarest, S.J. / Martinez-Yamout, M. / Chung, J. / Chen, H. / Xu, W. / Dyson, H.J. / Evans, R.M. / Wright, P.E.
CitationJournal: Nature / Year: 2002
Title: Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators.
Authors: Demarest, S.J. / Martinez-Yamout, M. / Chung, J. / Chen, H. / Xu, W. / Dyson, H.J. / Evans, R.M. / Wright, P.E.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nuclear receptor coactivator
B: CREB-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,6722
Polymers11,6722
Non-polymers00
Water0
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 least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein/peptide nuclear receptor coactivator / ACTR


Mass: 5103.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3(DNAY) / References: UniProt: Q9Y6Q9
#2: Protein CREB-BINDING PROTEIN /


Mass: 6568.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CBP / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3(DNAY) / References: UniProt: P45481

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3133D 13C-separated NOESY
1214D 13C-separated NOESY
2323D 15N-separated NOESY
34312C-filtered/13C-edited-NOESY
252HNHA
262HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM U-15N,13C-CBP:2059-2117 6mM 14N,12C-ACTR:1018-108810 mM Tris, 50 mM NaCl 95%H2O,5%D2O
23mM U-15N,12C-CBP:2059-2117 6mM 14N,12C-ACTR:1018-108810 mM Tris, 50 mM NaCl 95%H2O,5%D2O
33mM U-15N,13C-CBP:2059-2117 6mM 14N,12C-ACTR:1018-108810 mM Tris, 50 mM NaCl 100%D2O
42mM U-15N,13C-ACTR:1018-1088 4mM 14N,12C-CBP:2059-211710 mM Tris, 50 mM NaCl 95%H2O,5%D2O
52mM U-15N,12C-ACTR:1018-1088 4mM 14N,12C-CBP:2059-211710 mM Tris, 50 mM NaCl 95%H2O,5%D2O
62mM U-15N,13C-ACTR:1018-1088 4mM 14N,12C-CBP:2059-211710 mM Tris, 50 mM NaCl 100%D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
160 mM 6.6 ambient 31 K
260 mM 6.6 ambient 31 K
360 mM 6.6 ambient 31 K
460 mM 6.6 ambient 31 K
560 mM 6.6 ambient 31 K
660 mM 6.6 ambient 31 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 DRXBrukerDRX6001
Bruker AMXBrukerAMX5002
Bruker DMXBrukerDMX7503
Bruker DRXBrukerDRX8004
Bruker AMXBrukerAMX6005

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Wuthrich, et al.refinement
NMRPipe1Delagio, et al.processing
XwinNMR1Brukercollection
UXNMR1Brukercollection
Amber5Case, et al.refinement
NMRView3Johnson, B., et al.data analysis
RefinementMethod: Dyana, Sane, Amber / Software ordinal: 1
Details: 200 structures originally calculated using unambiguous restraints in Dyana followed by the addition of ambiguous restraints for simulated annealing of the top 100 Dyana structures in Amber. ...Details: 200 structures originally calculated using unambiguous restraints in Dyana followed by the addition of ambiguous restraints for simulated annealing of the top 100 Dyana structures in Amber. Best 20 structures selected to represent the structure of the ACTR/CBP complex.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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