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- PDB-8xtt: Nuclear receptor Nor1 ligand binding domain -

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Basic information

Entry
Database: PDB / ID: 8xtt
TitleNuclear receptor Nor1 ligand binding domain
ComponentsNuclear receptor subfamily 4 group A member 3
KeywordsNUCLEAR PROTEIN / Nuclear receptor
Function / homology
Function and homology information


positive regulation of mast cell activation by Fc-epsilon receptor signaling pathway / positive regulation of monocyte aggregation / cAMP response element binding / positive regulation of feeding behavior / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / common myeloid progenitor cell proliferation / nuclear glucocorticoid receptor binding / positive regulation of mast cell cytokine production / regulation of smooth muscle cell proliferation ...positive regulation of mast cell activation by Fc-epsilon receptor signaling pathway / positive regulation of monocyte aggregation / cAMP response element binding / positive regulation of feeding behavior / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / common myeloid progenitor cell proliferation / nuclear glucocorticoid receptor binding / positive regulation of mast cell cytokine production / regulation of smooth muscle cell proliferation / cellular respiration / cellular response to leptin stimulus / positive regulation of D-glucose transmembrane transport / positive regulation of vascular associated smooth muscle cell migration / nuclear steroid receptor activity / mast cell degranulation / positive regulation of cardiac muscle hypertrophy / fat cell differentiation / platelet-derived growth factor receptor signaling pathway / animal organ regeneration / energy homeostasis / positive regulation of vascular associated smooth muscle cell proliferation / gastrulation / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Nuclear Receptor transcription pathway / nuclear receptor activity / cellular response to catecholamine stimulus / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Orphan nuclear receptor, NOR1 type / Orphan nuclear receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily ...Orphan nuclear receptor, NOR1 type / Orphan nuclear receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Nuclear receptor subfamily 4 group A member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYoo, J.Y. / Yoon, H.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Nuclear receptor Nor1 ligand binding domain
Authors: Yoo, J.Y. / Yoon, H.S.
History
DepositionJan 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Nuclear receptor subfamily 4 group A member 3


Theoretical massNumber of molelcules
Total (without water)27,8361
Polymers27,8361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear receptor subfamily 4 group A member 3 / Mitogen-induced nuclear orphan receptor / Neuron-derived orphan receptor 1 / Nuclear hormone receptor NOR-1


Mass: 27836.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A3, CHN, CSMF, MINOR, NOR1, TEC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92570
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.6 mM [U-99% 15N] Nor1-LBD, 90% H2O/10% D2O / Label: 15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: Nor1-LBD / Isotopic labeling: [U-99% 15N]
Sample conditionsIonic strength: 150 mM NaCl Not defined / Label: 15N labeling / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYWoonghee Leechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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