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- PDB-8cyo: Nurr1 Covalently Bound to a Synthetic Ligand, 10.25, via a Disulf... -

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Basic information

Entry
Database: PDB / ID: 8cyo
TitleNurr1 Covalently Bound to a Synthetic Ligand, 10.25, via a Disulfide Bond
ComponentsNuclear receptor subfamily 4 group A member 2
KeywordsTRANSCRIPTION / Disulfide Tethering
Function / homology
Function and homology information


general adaptation syndrome / habenula development / central nervous system neuron differentiation / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / regulation of dopamine metabolic process / : / midbrain dopaminergic neuron differentiation / nuclear glucocorticoid receptor binding / regulation of respiratory gaseous exchange ...general adaptation syndrome / habenula development / central nervous system neuron differentiation / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / regulation of dopamine metabolic process / : / midbrain dopaminergic neuron differentiation / nuclear glucocorticoid receptor binding / regulation of respiratory gaseous exchange / dopaminergic neuron differentiation / neuron maturation / dopamine biosynthetic process / fat cell differentiation / negative regulation of apoptotic signaling pathway / canonical Wnt signaling pathway / nuclear retinoid X receptor binding / response to amphetamine / adult locomotory behavior / post-embryonic development / neuron migration / SUMOylation of intracellular receptors / beta-catenin binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / negative regulation of neuron apoptotic process / transcription regulator complex / transcription by RNA polymerase II / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Orphan nuclear receptor, NURR type / Orphan nuclear receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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, NURR type / Orphan nuclear receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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
Chem-OBJ / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsBruning, J.M. / Liu, J. / England, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Nurr1 Covalently Bound to a Synthetic Ligand, 10.25, via a Disulfide Bond
Authors: Holder, P.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nuclear receptor subfamily 4 group A member 2
A: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,05310
Polymers56,5252
Non-polymers5288
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-72 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.110, 70.660, 42.410
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Nuclear receptor subfamily 4 group A member 2 / Immediate-early response protein NOT / Orphan nuclear receptor NURR1 / Transcriptionally-inducible ...Immediate-early response protein NOT / Orphan nuclear receptor NURR1 / Transcriptionally-inducible nuclear receptor


Mass: 28262.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2, NOT, NURR1, TINUR / Production host: Escherichia coli (E. coli) / References: UniProt: P43354
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OBJ / 2-(3,4-dichlorophenoxy)-N-(2-sulfanylethyl)acetamide


Mass: 280.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H11Cl2NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 10-14% (w/v) PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.41→49.5 Å / Num. obs: 23699 / % possible obs: 98.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06282 / Rpim(I) all: 0.02625 / Net I/σ(I): 17.1
Reflection shellResolution: 2.41→2.49 Å / Redundancy: 5.63 % / Rmerge(I) obs: 0.767 / Num. unique obs: 2050 / CC1/2: 0.674 / Rpim(I) all: 0.345 / Rrim(I) all: 0.844 / % possible all: 85.13

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
XDSdata reduction
XSCALEdata scaling
PHASER1.15.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVL

1ovl


Resolution: 2.41→49.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.249 --
Rwork0.213 --
obs-23695 98.5 %
Refinement stepCycle: LAST / Resolution: 2.41→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 23 58 3823

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