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- PDB-6dha: Crystal Structure of Human PPARgamma Ligand Binding Domain in Com... -

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Basic information

Entry
Database: PDB / ID: 6dha
TitleCrystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Hydroxy Pioglitazone (M-IV)
ComponentsPeroxisome proliferator-activated receptor gamma
Keywordstranscription/transcription inhibitor / Nuclear receptors / TZDs / Drug design / Therapeutic targets / TRANSCRIPTION / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane ...Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane / aerobic respiration / mitochondrial inner membrane / mitochondrion / nucleoplasm
Similarity search - Function
NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / Retinoid X Receptor / Retinoid X Receptor / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hydroxy Pioglitazone (M-IV) / nonanoic acid / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsShang, J. / Mosure, S.A. / Kojetin, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK101871 United States
CitationJournal: J. Med. Chem. / Year: 2019
Title: Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPAR gamma Drug Pioglitazone.
Authors: Mosure, S.A. / Shang, J. / Eberhardt, J. / Brust, R. / Zheng, J. / Griffin, P.R. / Forli, S. / Kojetin, D.J.
History
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 gamma
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0556
Polymers61,9942
Non-polymers1,0614
Water4,396244
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6864
Polymers30,9971
Non-polymers6893
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)31,3692
Polymers30,9971
Non-polymers3721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.080, 61.850, 119.670
Angle α, β, γ (deg.)90.000, 102.730, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 30997.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-GFV / Hydroxy Pioglitazone (M-IV) / (5S)-5-{[4-(2-{5-[(1S)-1-hydroxyethyl]pyridin-2-yl}ethoxy)phenyl]methyl}-1,3-thiazolidine-2,4-dione


Mass: 372.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N2O4S
#3: Chemical ChemComp-KNA / nonanoic acid


Mass: 158.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8M SODIUM CITRATE, 100mM TRIS, pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.88→51.116 Å / Num. obs: 53101 / % possible obs: 97.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 34.28 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 4.93
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.29 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRG

1prg


Resolution: 1.88→51.12 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.36
RfactorNum. reflection% reflection
Rfree0.255 1981 3.76 %
Rwork0.22 50723 -
obs0.222 52704 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.78 Å2 / Biso mean: 46.25 Å2 / Biso min: 19.87 Å2
Refinement stepCycle: final / Resolution: 1.88→51.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 74 244 4463
Biso mean--39.36 45.28 -
Num. residues----518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.9270.49051370.48463522365995
1.927-1.97910.39471390.36213526366596
1.9791-2.03740.31171390.2823560369997
2.0374-2.10310.31831390.27533582372197
2.1031-2.17830.30821420.27213592373497
2.1783-2.26550.35891360.30153566370296
2.2655-2.36860.28341400.25563571371197
2.3686-2.49350.28921410.23583633377498
2.4935-2.64970.26171440.23463670381498
2.6497-2.85430.29551420.22963651379399
2.8543-3.14150.2811450.23723700384599
3.1415-3.5960.2641430.20523654379798
3.596-4.53010.20671450.17443700384599
4.5301-51.13520.18761490.18033796394599

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