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- PDB-4whg: Crystal Structure of TR3 LBD in complex with Molecule 3 -

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Basic information

Entry
Database: PDB / ID: 4whg
TitleCrystal Structure of TR3 LBD in complex with Molecule 3
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION / LBD
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
1-(3,4,5-trihydroxyphenyl)octan-1-one / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsLi, F.W. / Cai, Q.X. / Li, A.Z. / Tian, X.Y. / Wang, W.J. / Wang, Y. / Hou, P.P. / Wu, Q. / Lin, T.W.
CitationJournal: Chem.Biol. / Year: 2015
Title: Induction of Autophagic Death in Cancer Cells by Agonizing TR3 and Attenuating Akt2 Activity
Authors: Wang, W.J. / Wang, Y. / Hou, P.P. / Li, F.W. / Zhou, B. / Chen, H.Z. / Bian, X.L. / Cai, Q.X. / Xing, Y.Z. / He, J.P. / Zhang, H. / Huang, P.Q. / Lin, T. / Wu, Q.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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 / citation / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,2038
Polymers57,4912
Non-polymers7136
Water5,657314
1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8372
Polymers28,7451
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3666
Polymers28,7451
Non-polymers6215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.551, 76.807, 128.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 30 - 267 / Label seq-ID: 12 - 249

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A and chains B).

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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 binding 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-3NB / 1-(3,4,5-trihydroxyphenyl)octan-1-one


Mass: 252.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG4000, Sodium citrate, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2014 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 39232 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Χ2: 1.418 / Net I/av σ(I): 19.667 / Net I/σ(I): 12.9 / Num. measured all: 155445
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.18-2.223.80.47619651.06898.2
2.22-2.263.80.41919191.14498.9
2.26-2.33.90.35719451.21498
2.3-2.353.90.30819441.21998.4
2.35-2.440.26219621.23398.8
2.4-2.4640.23519451.26999.1
2.46-2.5240.20519801.35199.4
2.52-2.584.10.17719701.499.5
2.58-2.664.10.15319731.48299.7
2.66-2.754.10.1319801.56699.8
2.75-2.844.20.11519771.4299.7
2.84-2.964.20.09819971.4799.5
2.96-3.094.20.09319741.60999.5
3.09-3.264.10.08120101.76399.1
3.26-3.463.90.06919531.78498.7
3.46-3.733.80.0619861.89797.6
3.73-4.13.80.05719801.52197.6
4.1-4.73.70.05119571.37895.7
4.7-5.913.90.04720121.23297.5
5.91-503.70.04618031.23382.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
Cootmodel building
PHASERphasing
HKLdata scaling
RefinementResolution: 2.18→37.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.37 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1807 4.6 %RANDOM
Rwork0.1851 37351 --
obs0.1874 37351 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.35 Å2 / Biso mean: 40.044 Å2 / Biso min: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20 Å2
2--0.58 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 2.18→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 36 314 3989
Biso mean--85.02 47.44 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193754
X-RAY DIFFRACTIONr_bond_other_d0.0070.023715
X-RAY DIFFRACTIONr_angle_refined_deg1.9712.0075078
X-RAY DIFFRACTIONr_angle_other_deg1.35838555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62823.247154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8315647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3091528
X-RAY DIFFRACTIONr_chiral_restr0.1320.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214106
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02816
X-RAY DIFFRACTIONr_mcbond_it3.7783.6921860
X-RAY DIFFRACTIONr_mcbond_other3.7783.691859
X-RAY DIFFRACTIONr_mcangle_it5.2135.4832315
Refine LS restraints NCS

Ens-ID: 1 / Number: 13162 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.158→2.214 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 103 -
Rwork0.236 2320 -
all-2423 -
obs--82.44 %

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