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

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Basic information

Entry
Database: PDB / ID: 6dgo
TitleCrystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Troglitazone
ComponentsPeroxisome proliferator-activated receptor gamma
Keywordstranscription/transcription inhibitor / Nuclear receptors / TZDs / Drug design / Therapeutic targets / 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
Chem-GD4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShang, J. / 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: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Quantitative structural assessment of graded receptor agonism.
Authors: Shang, J. / Brust, R. / Griffin, P.R. / Kamenecka, T.M. / Kojetin, D.J.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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)63,3413
Polymers62,8992
Non-polymers4421
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-0 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.810, 62.070, 118.760
Angle α, β, γ (deg.)90.000, 102.100, 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: 31449.520 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-GD4 / (5S)-5-[(4-{[(2R)-6-hydroxy-2,5,7,8-tetramethyl-3,4-dihydro-2H-1-benzopyran-2-yl]methoxy}phenyl)methyl]-1,3-thiazolidine-2,4-dione / Troglitazone (isoform)


Mass: 441.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27NO5S

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.8M SODIUM CITRATE, 100mM MOPS, pH 7.6

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→45.374 Å / Num. obs: 12003 / % possible obs: 98.55 % / Redundancy: 1.8 % / Net I/σ(I): 8.48
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1150 / % possible all: 97.71

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Processing

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

1prg


Resolution: 3.1→45.374 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 1200 10 %
Rwork0.1936 10801 -
obs0.2022 12001 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.8 Å2 / Biso mean: 25.1537 Å2 / Biso min: 2.71 Å2
Refinement stepCycle: final / Resolution: 3.1→45.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 31 0 4172
Biso mean--29.47 --
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134244
X-RAY DIFFRACTIONf_angle_d1.2185716
X-RAY DIFFRACTIONf_chiral_restr0.057658
X-RAY DIFFRACTIONf_plane_restr0.012718
X-RAY DIFFRACTIONf_dihedral_angle_d17.7121619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.22410.35071280.2511152128098
3.2241-3.37080.29751310.23441185131698
3.3708-3.54840.3491320.21041181131399
3.5484-3.77060.28981330.19621203133699
3.7706-4.06160.27031340.18451202133698
4.0616-4.470.24361330.16841195132899
4.47-5.11610.2741360.17031218135499
5.1161-6.44280.26521340.20021208134299
6.4428-45.37890.19071390.16361257139699
Refinement TLS params.Method: refined / Origin x: 21.6425 Å / Origin y: 45.111 Å / Origin z: 25.3652 Å
111213212223313233
T0.0233 Å20.0442 Å2-0.0063 Å2-0.0163 Å20.0373 Å2--0.0209 Å2
L0.008 °2-0.0014 °20.0035 °2-0.0019 °20.0011 °2--0.0067 °2
S-0.0023 Å °-0.0079 Å °-0.0069 Å °0.003 Å °0.0164 Å °0.0061 Å °-0.0074 Å °0.0114 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA207 - 474
2X-RAY DIFFRACTION1allB207 - 475
3X-RAY DIFFRACTION1allA501

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