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- PDB-6dda: Nurr1 Covalently Modified by a Dopamine Metabolite -

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Basic information

Entry
Database: PDB / ID: 6dda
TitleNurr1 Covalently Modified by a Dopamine Metabolite
Components(Nuclear receptor subfamily 4 group A member 2) x 2
KeywordsTRANSCRIPTION / Nurr1 / Dopamine / Cysteine Adduct / Dihydroxyindole
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 / Retinoid X Receptor / Retinoid X 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 ...Orphan nuclear receptor, NURR type / Orphan nuclear receptor / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / 5-hydroxy-1,2-dihydro-6H-indol-6-one / : / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsBruning, J.M. / Wang, Y. / Otrabella, F. / Boxue, T. / Liu, H. / Bhattacharya, P. / Guo, S. / Holton, J.M. / Fletterick, R.J. / Jacobson, M.P. / England, P.M.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.
Authors: Bruning, J.M. / Wang, Y. / Oltrabella, F. / Tian, B. / Kholodar, S.A. / Liu, H. / Bhattacharya, P. / Guo, S. / Holton, J.M. / Fletterick, R.J. / Jacobson, M.P. / England, P.M.
History
DepositionMay 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support

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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
C: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,24018
Polymers92,0383
Non-polymers1,20215
Water0
1
B: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8914
Polymers30,6631
Non-polymers2273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2588
Polymers30,7111
Non-polymers5477
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0916
Polymers30,6631
Non-polymers4285
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.586, 80.586, 225.805
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-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: 30663.330 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: 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: 30711.330 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-G7J / 5-hydroxy-1,2-dihydro-6H-indol-6-one


Mass: 149.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H7NO2
#5: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br

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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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES, 202.9mM potassium bromide, 18.45% PEG 3350
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.2→40.29 Å / Num. obs: 14697 / % possible obs: 99.6 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.201 / Net I/σ(I): 13.74
Reflection shellResolution: 3.2→3.31 Å / % possible all: 99.6

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 3.2→40.29 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection
Rfree0.2945 -
Rwork0.2497 -
obs-14697
Refinement stepCycle: LAST / Resolution: 3.2→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 45 0 5525

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