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- PDB-7c4o: Solution structure of the Orange domain from human protein HES1 -

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Basic information

Entry
Database: PDB / ID: 7c4o
TitleSolution structure of the Orange domain from human protein HES1
ComponentsTranscription factor HES-1
KeywordsSIGNALING PROTEIN / dimer / solution structure
Function / homology
Function and homology information


trochlear nerve development / stomach neuroendocrine cell differentiation / negative regulation of stomach neuroendocrine cell differentiation / N-box binding / comma-shaped body morphogenesis / S-shaped body morphogenesis / renal interstitial fibroblast development / negative regulation of cell fate determination / negative regulation of pancreatic A cell differentiation / positive regulation of mitotic cell cycle, embryonic ...trochlear nerve development / stomach neuroendocrine cell differentiation / negative regulation of stomach neuroendocrine cell differentiation / N-box binding / comma-shaped body morphogenesis / S-shaped body morphogenesis / renal interstitial fibroblast development / negative regulation of cell fate determination / negative regulation of pancreatic A cell differentiation / positive regulation of mitotic cell cycle, embryonic / regulation of timing of neuron differentiation / pancreatic A cell differentiation / midbrain-hindbrain boundary morphogenesis / metanephric nephron tubule morphogenesis / common bile duct development / negative regulation of amacrine cell differentiation / ureteric bud morphogenesis / hindbrain morphogenesis / lateral inhibition / amacrine cell differentiation / oculomotor nerve development / ascending aorta morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / glomerulus vasculature development / adenohypophysis development / vascular associated smooth muscle cell development / cell morphogenesis involved in neuron differentiation / HLH domain binding / negative regulation of pro-B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / Cajal-Retzius cell differentiation / pharyngeal arch artery morphogenesis / regulation of secondary heart field cardioblast proliferation / negative regulation of calcium ion import / inner ear receptor cell stereocilium organization / NOTCH2 intracellular domain regulates transcription / establishment of epithelial cell polarity / telencephalon development / inner ear auditory receptor cell differentiation / neuronal stem cell population maintenance / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / response to thyroid hormone / forebrain radial glial cell differentiation / cell fate determination / positive regulation of BMP signaling pathway / negative regulation of stem cell differentiation / JUN kinase binding / regulation of epithelial cell proliferation / embryonic heart tube morphogenesis / response to alkaloid / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / regulation of receptor signaling pathway via JAK-STAT / NOTCH4 Intracellular Domain Regulates Transcription / regulation of fat cell differentiation / labyrinthine layer blood vessel development / NOTCH3 Intracellular Domain Regulates Transcription / anterior/posterior pattern specification / artery morphogenesis / cellular response to fatty acid / ventricular septum development / negative regulation of glial cell proliferation / smoothened signaling pathway / midbrain development / ventricular septum morphogenesis / cochlea development / positive regulation of Notch signaling pathway / outflow tract morphogenesis / E-box binding / RUNX2 regulates osteoblast differentiation / somatic stem cell population maintenance / negative regulation of neuron differentiation / regulation of neurogenesis / regulation of protein-containing complex assembly / positive regulation of DNA binding / cellular response to interleukin-1 / BMP signaling pathway / T cell proliferation / positive regulation of T cell proliferation / cell maturation / positive regulation of tyrosine phosphorylation of STAT protein / Notch signaling pathway / cellular response to nerve growth factor stimulus / transcription corepressor binding / thymus development / liver development / positive regulation of receptor signaling pathway via JAK-STAT / lung development / negative regulation of forebrain neuron differentiation / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / sequence-specific double-stranded DNA binding / cell migration
Similarity search - Function
Orange domain / Hairy Orange / Orange domain profile. / Orange domain / Helix-loop-helix DNA-binding domain / 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.
Similarity search - Domain/homology
Transcription factor HES-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFan, J.S. / Nayak, A. / Swaminathan, K.
CitationJournal: Am J Pathol / Year: 2022
Title: Induction of Transcriptional Inhibitor Hairy and Enhancer of Split Homolog-1 and the Related Repression of Tumor-Suppressor Thioredoxin-Interacting Protein Are Important Components of Cell- ...Title: Induction of Transcriptional Inhibitor Hairy and Enhancer of Split Homolog-1 and the Related Repression of Tumor-Suppressor Thioredoxin-Interacting Protein Are Important Components of Cell-Transformation Program Imposed by Oncogenic Kinase Nucleophosmin-Anaplastic Lymphoma Kinase.
Authors: Zhang, Q. / Wang, H.Y. / Nayak, A. / Nunez-Cruz, S. / Slupianek, A. / Liu, X. / Basappa, J. / Fan, J.S. / Chekol, S. / Nejati, R. / Bogusz, A.M. / Turner, S.D. / Swaminathan, K. / Wasik, M.A.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: Transcription factor HES-1
B: Transcription factor HES-1


Theoretical massNumber of molelcules
Total (without water)10,7102
Polymers10,7102
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1960 Å2
ΔGint-28 kcal/mol
Surface area6150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Transcription factor HES-1 / Class B basic helix-loop-helix protein 39 / bHLHb39 / Hairy and enhancer of split 1 / Hairy homolog ...Class B basic helix-loop-helix protein 39 / bHLHb39 / Hairy and enhancer of split 1 / Hairy homolog / Hairy-like protein / hHL


Mass: 5355.138 Da / Num. of mol.: 2 / Fragment: orange domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HES1, BHLHB39, HL, HRY / Production host: Escherichia coli (E. coli) / References: UniProt: Q14469

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D 1H-15N NOESY
151isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-99% 13C; U-99% 15N] orange domain, 90% H2O/10% D2O
Label: CN-sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: orange domain / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 mM / Ionic strength err: 0.1 / Label: con_1 / pH: 6.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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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
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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