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- PDB-1ovl: Crystal Structure of Nurr1 LBD -

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Basic information

Entry
Database: PDB / ID: 1ovl
TitleCrystal Structure of Nurr1 LBD
Components(Orphan nuclear receptor NURR1 (MSE ...) x 2
KeywordsTRANSCRIPTION / Nuur1 / LBD
Function / homology
Function and homology information


general adaptation syndrome / habenula development / cellular response to corticotropin-releasing hormone stimulus / central nervous system neuron differentiation / central nervous system projection neuron axonogenesis / nuclear glucocorticoid receptor binding / regulation of dopamine metabolic process / midbrain dopaminergic neuron differentiation / regulation of respiratory gaseous exchange / dopaminergic neuron differentiation ...general adaptation syndrome / habenula development / cellular response to corticotropin-releasing hormone stimulus / central nervous system neuron differentiation / central nervous system projection neuron axonogenesis / nuclear glucocorticoid receptor binding / regulation of dopamine metabolic process / midbrain dopaminergic neuron differentiation / 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 / post-embryonic development / adult locomotory behavior / SUMOylation of intracellular receptors / neuron migration / 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 / transcription regulator complex / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / 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 / Double treble clef zinc finger, C4 type / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / IODIDE ION / : / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsWang, Z. / Liu, J. / Walker, N.
CitationJournal: Nature / Year: 2003
Title: Structure and Function of Nurr1 identifies a Class of Ligand-Independent Nuclear Receptors
Authors: Wang, Z. / Benoit, G. / Liu, J. / Prasad, S. / Aarnisalo, P. / Liu, X. / Xu, H. / Walker, N. / Perlmann, T.
History
DepositionMar 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orphan nuclear receptor NURR1 (MSE 414, 496, 511)
B: Orphan nuclear receptor NURR1 (MSE 496, 511)
C: Orphan nuclear receptor NURR1 (MSE 496, 511)
D: Orphan nuclear receptor NURR1 (MSE 414, 496, 511)
E: Orphan nuclear receptor NURR1 (MSE 496, 511)
F: Orphan nuclear receptor NURR1 (MSE 496, 511)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,16634
Polymers184,2086
Non-polymers1,95828
Water10,124562
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.383, 80.383, 227.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Orphan nuclear receptor NURR1 (MSE ... , 2 types, 6 molecules ADBCEF

#1: Protein Orphan nuclear receptor NURR1 (MSE 414, 496, 511) / Immediate-early response protein NOT / Transcriptionally inducible nuclear receptor


Mass: 30670.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 OR NURR1 OR TINUR OR NOT / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P43354
#2: Protein
Orphan nuclear receptor NURR1 (MSE 496, 511) / Immediate-early response protein NOT / Transcriptionally inducible nuclear receptor


Mass: 30716.936 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 OR NURR1 OR TINUR OR NOT / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P43354

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Non-polymers , 4 types, 590 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 46.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG3350,KBr, Hepes, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-7 mg/mlprotein1drop
220 mMTris-HCl1droppH7.9
3100 mM1dropNaCl
42 mMEDTA1drop
55 mMdithiothreitol1drop
618 %(w/v)PEG33501reservoir
70.1 MHEPES1reservoirpH6.5
80.2 M1reservoirKBr

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2001
RadiationMonochromator: Double cyrstal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→34.7 Å / Num. all: 287222 / Num. obs: 82388 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.072 / Net I/σ(I): 6.2
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.4 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 287222 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNXrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4117 -Radom
Rwork0.217 ---
all0.231 83435 --
obs0.231 82321 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11113 0 28 562 11703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.006
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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