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- PDB-4a4w: Ligand binding domain of human PPAR gamma in complex with amorfrutin B -

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Basic information

Entry
Database: PDB / ID: 4a4w
TitleLigand binding domain of human PPAR gamma in complex with amorfrutin B
ComponentsPEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
KeywordsRECEPTOR / AGONIST / DIABETES / INSULIN RESISTANCE
Function / homology
Function and homology information


prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding ...prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / Regulation of PTEN gene transcription / positive regulation of apoptotic signaling pathway / transcription coregulator binding / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / negative regulation of transforming growth factor beta receptor signaling pathway / fatty acid metabolic process / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of miRNA transcription / regulation of blood pressure / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to insulin stimulus / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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
AMORFRUTIN B / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsde Groot, J.C. / Weidner, C. / Krausze, J. / Kawamoto, K. / Schroeder, F.C. / Sauer, S. / Buessow, K.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural Characterization of Amorfrutins Bound to the Peroxisome Proliferator-Activated Receptor Gamma.
Authors: De Groot, J.C. / Weidner, C. / Krausze, J. / Kawamoto, K. / Schroeder, F.C. / Sauer, S. / Bussow, K.
History
DepositionOct 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2054
Polymers65,3882
Non-polymers8172
Water4,882271
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers32,6941
Non-polymers4091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers32,6941
Non-polymers4091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.140, 60.860, 117.600
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.09906, -0.97711, 0.18826), (-0.98416, -0.12415, -0.12653), (0.147, -0.17274, -0.97394)
Vector: -13.86474, -23.26374, -46.05626)

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Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA / PPAR-GAMMA / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3


Mass: 32693.824 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 195-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-YFB / AMORFRUTIN B


Mass: 408.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H32O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.46 Å3/Da / Density % sol: 50.11 % / Description: NONE
Crystal growpH: 8 / Details: 0.8 M TRI-SODIUM CITRATE 0.1 M IMIDAZOLE, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419
DetectorType: RIGAKU-MSC SATURN 944 PLUS / Detector: CCD / Date: Sep 30, 2010
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. obs: 42829 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.4 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PRG

1prg


Resolution: 2→29.41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.197 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23436 2142 5 %RANDOM
Rwork0.20309 ---
obs0.2047 40687 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.02 Å2
2--1.53 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 60 271 4551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1862.0036082
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.175562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50425.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41915883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3221516
X-RAY DIFFRACTIONr_chiral_restr0.080.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213309
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7631.52696
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40324391
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81431799
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.14.51671
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
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 154 -
Rwork0.271 2932 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6403-0.7573-0.67010.36550.42612.1482-0.1787-0.1227-0.04280.11430.0975-0.00150.02890.17630.08120.2661-0.0212-0.00790.2141-0.0010.2191-3.98949.177-9.0061
25.4043-1.0318-6.15271.0291.89417.72820.4158-0.070.65690.08880.2083-0.0197-0.65010.3241-0.62410.71370.0205-0.16280.090.04990.2645-18.692927.5727-8.8156
30.623-0.2319-0.32320.52990.12751.1612-0.04080.0418-0.05910.04210.04610.0816-0.0536-0.0992-0.00530.1974-0.0376-0.00660.21020.00250.2205-11.82548.979-19.0895
42.4255-4.09570.54937.2722-0.97330.34330.04480.1593-0.1314-0.0085-0.05820.26210.046-0.11350.01340.1738-0.0806-0.00820.26170.00470.2745-22.19978.6742-20.9761
55.7787-7.4199-0.50549.52990.65030.04720.29350.2437-0.45-0.4039-0.32280.6014-0.0587-0.02230.02930.3683-0.0025-0.01950.20440.05150.2752-20.323524.1629-26.1783
61.2206-0.3092-0.04071.9511-0.89162.88790.02890.2802-0.11080.002-0.0012-0.06790.38080.1371-0.02760.2368-0.04820.00380.1677-0.0430.2471-22.1948-22.2047-33.4175
72.4373-0.3562-2.19780.8071-1.39147.9840.31910.8273-0.5706-0.0743-0.32050.06170.3257-0.76420.00140.2183-0.0537-0.20380.5084-0.08890.2917-41.0925-11.6996-51.6331
80.72490.0454-0.0120.3444-0.06560.98060.02870.0910.0438-0.018-0.0101-0.0073-0.0511-0.0602-0.01870.2031-0.04620.01110.208-0.00080.2181-28.865-9.8466-31.4895
910.7101-4.42040.53682.9790.460.43140.09580.10250.5153-0.2245-0.1214-0.2119-0.1248-0.03110.02560.2494-0.01660.05340.22610.05640.2603-25.3777-0.8042-29.7972
100.62753.3512-0.54718.5579-2.98320.4833-0.01340.10220.16870.19940.17680.3961-0.052-0.0544-0.16340.4538-0.12440.20010.21280.21250.4888-51.1276-1.9024-32.1015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A203 - 253
2X-RAY DIFFRACTION2A254 - 291
3X-RAY DIFFRACTION3A292 - 428
4X-RAY DIFFRACTION4A429 - 460
5X-RAY DIFFRACTION5A461 - 477
6X-RAY DIFFRACTION6B206 - 239
7X-RAY DIFFRACTION7B240 - 270
8X-RAY DIFFRACTION8B275 - 428
9X-RAY DIFFRACTION9B429 - 456
10X-RAY DIFFRACTION10B457 - 474

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