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- PDB-4ree: Crystal Structure of TR3 LBD in complex with Molecule 6 -

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Basic information

Entry
Database: PDB / ID: 4ree
TitleCrystal Structure of TR3 LBD in complex with Molecule 6
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 / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / 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 / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / 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 / Constitutive Signaling by AKT1 E17K in Cancer / skeletal muscle cell differentiation / 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 / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / 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-(2,3,4-trihydroxyphenyl)nonan-1-one / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 2.37 Å
AuthorsLi, F.W. / Cai, Q.X. / Li, A.Z. / Tian, X.Y. / Wang, W.J. / Yuan, W. / 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 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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)57,7716
Polymers57,2282
Non-polymers5434
Water2,738152
1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7983
Polymers28,6141
Non-polymers1842
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)28,9733
Polymers28,6141
Non-polymers3582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-15 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.829, 76.615, 128.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B31 - 267
2010A31 - 267

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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: 28614.113 Da / Num. of mol.: 2 / Fragment: UNP residues 351-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRP1, HMR, NAK1, NR4A1 / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-3MZ / 1-(2,3,4-trihydroxyphenyl)nonan-1-one


Mass: 266.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.22 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.2
Details: PEG4000, Sodium citrate, Glycerol, pH 4.2, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / 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: 2.37→50 Å / Num. all: 30674 / Num. obs: 30429 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.37-2.414.20.505199.9
2.41-2.454.20.4461100
2.45-2.54.20.3911100
2.5-2.554.20.327199.9
2.55-2.614.20.31199.9
2.61-2.674.20.2551100
2.67-2.744.20.225199.9
2.74-2.814.20.202199.9
2.81-2.894.20.17199.8
2.89-2.994.20.15199.5
2.99-3.094.30.144199.3
3.09-3.224.20.118199.7
3.22-3.364.20.104199.7
3.36-3.544.20.093199.7
3.54-3.764.20.085199.2
3.76-4.054.20.071199.3
4.05-4.464.20.057199.5
4.46-5.14.20.055198.9
5.1-6.434.60.061100
6.43-5040.064191.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.37→37.21 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.257 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2574 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24114 1548 5.1 %RANDOM
Rwork0.1995 ---
obs0.20163 28811 98.97 %-
all-30674 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.426 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-0 Å2
2--0.31 Å2-0 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.37→37.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 37 152 3843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193754
X-RAY DIFFRACTIONr_bond_other_d0.0060.023720
X-RAY DIFFRACTIONr_angle_refined_deg1.8062.0045081
X-RAY DIFFRACTIONr_angle_other_deg1.31638565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88623.226155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.19415651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4431528
X-RAY DIFFRACTIONr_chiral_restr0.1030.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214122
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02822
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7755.0941863
X-RAY DIFFRACTIONr_mcbond_other4.775.0921862
X-RAY DIFFRACTIONr_mcangle_it6.7547.5942320
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.9455.5741891
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13325 / 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: 2.371→2.433 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 106 -
Rwork0.239 2059 -
obs--97.26 %

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