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- PDB-2b50: Human Nuclear Receptor-Ligand Complex 2 -

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Basic information

Entry
Database: PDB / ID: 2b50
TitleHuman Nuclear Receptor-Ligand Complex 2
ComponentsPeroxisome proliferator activated receptor delta
KeywordsGENE REGULATION / Nuclear Receptor / Protein-Ligand Complex / PPAR
Function / homology
Function and homology information


fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / positive regulation of myoblast proliferation / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of fatty acid oxidation / phospholipid biosynthetic process / Carnitine shuttle / negative regulation of myoblast differentiation / response to vitamin A / Signaling by Retinoic Acid / positive regulation of fatty acid metabolic process / nuclear steroid receptor activity / fatty acid beta-oxidation / negative regulation of cholesterol storage / cell-substrate adhesion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / adipose tissue development / NF-kappaB binding / cellular response to nutrient levels / fatty acid transport / response to glucose / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / cholesterol metabolic process / negative regulation of miRNA transcription / response to activity / fatty acid metabolic process / generation of precursor metabolites and energy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / wound healing / transcription coactivator binding / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / vasodilation / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / lipid binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated 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. ...Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated 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
heptyl beta-D-glucopyranoside / VACCENIC ACID / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFyffe, S.A. / Alphey, M.S. / Buetow, L. / Smith, T.K. / Ferguson, M.A.J. / Sorensen, M.D. / Bjorkling, F. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Recombinant Human PPAR-beta/delta Ligand-binding Domain is Locked in an Activated Conformation by Endogenous Fatty Acids
Authors: Fyffe, S.A. / Alphey, M.S. / Buetow, L. / Smith, T.K. / Ferguson, M.A.J. / Sorensen, M.D. / Bjorkling, F. / Hunter, W.N.
History
DepositionSep 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator activated receptor delta
B: Peroxisome proliferator activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2628
Polymers62,0602
Non-polymers1,2026
Water9,350519
1
A: Peroxisome proliferator activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9095
Polymers31,0301
Non-polymers8794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3533
Polymers31,0301
Non-polymers3232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.776, 92.084, 95.017
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 2 biological units the aymmetric unit (chains A and B)

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Components

#1: Protein Peroxisome proliferator activated receptor delta / PPAR-delta / PPAR- beta / Nuclear hormone receptor 1 / NUC1 / NUCI


Mass: 31030.061 Da / Num. of mol.: 2 / Fragment: residues 205-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: Q03181
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-B7G / heptyl beta-D-glucopyranoside / HEPTYL-BETA-D-GLUCOPYRANOSIDE / heptyl beta-D-glucoside / heptyl D-glucoside / heptyl glucoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 8000, 200mM KCl, 40mM bis-tris-propane pH 8.5, 2.5% 1,2-propanediol, 0.5% n-heptyl-B-D-glucopyranoside, 1mM EDTA, 10mM DTT, vapour diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 65 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.939261 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939261 Å / Relative weight: 1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→94.49 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.901 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2251 5 %RANDOM
Rwork0.197 ---
all0.199 42441 --
obs0.199 44692 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.6 Å2
2--2.09 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2→94.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 80 519 4797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224364
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9795881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27924.074189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04715780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1331522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023172
X-RAY DIFFRACTIONr_nbd_refined0.2080.22103
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2411
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.251
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1430.22
X-RAY DIFFRACTIONr_mcbond_it0.6721.52706
X-RAY DIFFRACTIONr_mcangle_it1.12324237
X-RAY DIFFRACTIONr_scbond_it1.62231845
X-RAY DIFFRACTIONr_scangle_it2.634.51644
LS refinement shellHighest resolution: 2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 163 -
Rwork0.284 3081 -
all-3244 -
obs--96.4 %

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