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- PDB-3v3q: Crystal Structure of Human Nur77 Ligand-binding Domain in Complex... -

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Basic information

Entry
Database: PDB / ID: 3v3q
TitleCrystal Structure of Human Nur77 Ligand-binding Domain in Complex with Ethyl 2-[2,3,4 trimethoxy-6(1-octanoyl)phenyl]acetate
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION/antagonist / orphan nuclear receptor / protein-antagonist complex / TRANSCRIPTION / TRANSCRIPTION-antagonist complex
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR 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, HMR 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
ethyl (2,3,4-trimethoxy-6-octanoylphenyl)acetate / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsZhang, Q. / Shi, C. / Yang, K. / Chen, Y. / Zhan, Y. / Wu, Q. / Lin, T.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: The orphan nuclear receptor Nur77 regulates LKB1 localization and activates AMPK
Authors: Zhan, Y. / Chen, Y. / Zhang, Q. / Zhuang, J. / Tian, M. / Chen, H. / Zhang, L. / Zhang, H. / He, J. / Wang, W. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A. / Xin, Y. / Li, T.Y. / Yang, ...Authors: Zhan, Y. / Chen, Y. / Zhang, Q. / Zhuang, J. / Tian, M. / Chen, H. / Zhang, L. / Zhang, H. / He, J. / Wang, W. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A. / Xin, Y. / Li, T.Y. / Yang, J.Y. / Zheng, Z. / Yu, C. / Lin, S. / Chang, C. / Huang, P. / Lin, T. / Wu, Q.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: Nuclear receptor subfamily 4 group A member 1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6439
Polymers57,4912
Non-polymers1,1527
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-31 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.242, 76.773, 129.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor subfamily 4 group A member 1 / Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR ...Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR / Orphan nuclear receptor TR3 / ST-59 / Testicular receptor 3


Mass: 28745.305 Da / Num. of mol.: 2 / Fragment: ligand-bingding domain, UNP residues 351-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22736
#2: Chemical ChemComp-TMY / ethyl (2,3,4-trimethoxy-6-octanoylphenyl)acetate


Mass: 380.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 7% PEG 6000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→48.73 Å / Num. obs: 34891 / % possible obs: 93.6 % / Rmerge(I) obs: 0.07
Reflection shellHighest resolution: 2.22 Å / % possible all: 93.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.33 Å
Translation2.5 Å49.33 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V3E

3v3e


Resolution: 2.22→48.73 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2808 / WRfactor Rwork: 0.2035 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7969 / SU B: 6.817 / SU ML: 0.172 / SU R Cruickshank DPI: 0.2486 / SU Rfree: 0.2369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 1752 5 %RANDOM
Rwork0.2092 ---
obs0.2131 33113 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.95 Å2 / Biso mean: 35.7602 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.22→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 79 397 4209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193926
X-RAY DIFFRACTIONr_angle_refined_deg1.9372.0155311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73923.455165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84715675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4431529
X-RAY DIFFRACTIONr_chiral_restr0.1250.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212903
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 119 -
Rwork0.259 2350 -
all-2469 -
obs--97.67 %

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