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- PDB-6fzj: PPAR gamma mutant complex -

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Basic information

Entry
Database: PDB / ID: 6fzj
TitlePPAR gamma mutant complex
Components(Peroxisome proliferator-activated receptor ...) x 2
KeywordsTRANSCRIPTION / nuclear receptor
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-EDK / IODIDE ION / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsRochel, N.
CitationJournal: Nat Commun / Year: 2019
Title: Recurrent activating mutations of PPAR gamma associated with luminal bladder tumors.
Authors: Rochel, N. / Krucker, C. / Coutos-Thevenot, L. / Osz, J. / Zhang, R. / Guyon, E. / Zita, W. / Vanthong, S. / Hernandez, O.A. / Bourguet, M. / Badawy, K.A. / Dufour, F. / Peluso-Iltis, C. / ...Authors: Rochel, N. / Krucker, C. / Coutos-Thevenot, L. / Osz, J. / Zhang, R. / Guyon, E. / Zita, W. / Vanthong, S. / Hernandez, O.A. / Bourguet, M. / Badawy, K.A. / Dufour, F. / Peluso-Iltis, C. / Heckler-Beji, S. / Dejaegere, A. / Kamoun, A. / de Reynies, A. / Neuzillet, Y. / Rebouissou, S. / Beraud, C. / Lang, H. / Massfelder, T. / Allory, Y. / Cianferani, S. / Stote, R.H. / Radvanyi, F. / Bernard-Pierrot, I.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Peroxisome proliferator-activated receptor gamma
C: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,29712
Polymers65,9114
Non-polymers1,3878
Water7,278404
1
A: Peroxisome proliferator-activated receptor gamma
C: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6847
Polymers32,9552
Non-polymers7295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-40 kcal/mol
Surface area13620 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor gamma
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6135
Polymers32,9552
Non-polymers6583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-19 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.270, 126.430, 54.720
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Peroxisome proliferator-activated receptor ... , 2 types, 4 molecules ABCD

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


Mass: 31431.480 Da / Num. of mol.: 2 / Mutation: M280I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37231
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1523.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 412 molecules

#3: Chemical ChemComp-EDK / (2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid


Mass: 495.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H29N3O4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 550 MME, 10% PEG 20 000, 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 0.1 M sodium Hepes / MOPS pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.011→15.18 Å / Num. obs: 46076 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.63 Å2 / Rmerge(I) obs: 0.1146 / Net I/σ(I): 9.77
Reflection shellResolution: 2.011→2.08 Å / Rmerge(I) obs: 0.7271

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRG

1prg


Resolution: 2.011→15.18 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.56
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2278 4.99 %RANDOM
Rwork0.175 ---
obs0.176 45617 97.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.011→15.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 80 404 4959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074817
X-RAY DIFFRACTIONf_angle_d0.8316519
X-RAY DIFFRACTIONf_dihedral_angle_d14.8423057
X-RAY DIFFRACTIONf_chiral_restr0.046752
X-RAY DIFFRACTIONf_plane_restr0.005882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0105-2.05410.3791060.30522010X-RAY DIFFRACTION73
2.0541-2.10180.3451440.2872774X-RAY DIFFRACTION99
2.1018-2.15420.32151430.25882709X-RAY DIFFRACTION99
2.1542-2.21230.31241440.23942736X-RAY DIFFRACTION99
2.2123-2.27720.31951430.24652756X-RAY DIFFRACTION98
2.2772-2.35040.27921430.22922703X-RAY DIFFRACTION98
2.3504-2.43410.30441430.23792722X-RAY DIFFRACTION98
2.4341-2.53110.29481450.22272745X-RAY DIFFRACTION98
2.5311-2.64580.28291440.2132748X-RAY DIFFRACTION99
2.6458-2.78440.24441460.18972762X-RAY DIFFRACTION99
2.7844-2.95770.24411440.16772742X-RAY DIFFRACTION100
2.9577-3.18410.24281470.16742792X-RAY DIFFRACTION100
3.1841-3.5010.21291460.1572786X-RAY DIFFRACTION100
3.501-3.99950.19191470.13062774X-RAY DIFFRACTION99
3.9995-5.00870.14121450.12132770X-RAY DIFFRACTION99
5.0087-15.17930.17471480.14822811X-RAY DIFFRACTION99
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)
12.27011.2582.36931.76142.0734.777-0.1063-0.11140.4503-0.0828-0.09630.2127-0.5201-0.06990.14740.3134-0.00670.05470.21420.00180.3039-13.803338.2053-9.1792
21.2540.17950.09691.26510.25381.61530.0066-0.0225-0.01650.06690.0081-0.0450.07240.0775-0.01610.182-0.00640.02180.1720.00390.1726-16.778423.0112-10.4758
38.0881-0.48783.70052.7026-3.36587.44690.085-0.8764-0.38050.4197-0.12910.11350.0912-0.4990.08290.268-0.02040.08470.35890.0160.2589-27.145224.00093.9928
44.80240.059-0.77463.1724-3.13177.3407-0.02720.5962-0.0274-1.18250.1421-0.07610.26280.0179-0.09960.5155-0.01710.04340.341-0.05090.1697-4.8629-6.0737-30.8548
53.04064.9107-0.26837.9458-0.62016.7198-0.02720.1884-0.4821-0.37890.11170.37791.0644-0.5507-0.0480.4168-0.0627-0.030.32120.04710.2466-16.4409-16.1038-17.8417
64.2662.2378-2.02923.0436-1.74812.4912-0.0723-0.2226-0.47380.0943-0.1074-0.24660.24220.06770.1730.28220.03440.00650.2263-0.00670.2451-6.6678-13.9413-7.1234
73.10610.8089-0.09834.369-2.53436.8101-0.0651-0.25660.1790.43990.11830.4741-0.4239-0.2946-0.0860.20950.00740.04910.23040.01140.2817-19.0059-9.7118-3.6451
84.95041.1482.28563.4129-0.01584.9805-0.13920.29870.2825-0.40950.07770.2754-0.1816-0.10690.06350.2830.0121-0.0080.18470.01430.1939-7.32882.8108-23.2891
94.1221-1.79733.66074.2617-3.42414.2068-0.3932-0.59690.4850.68480.04910.047-1.087-0.5120.39580.3680.00290.03170.2515-0.05260.2946-10.68682.4456-5.3274
106.6466-1.2694-1.55715.88291.91326.6394-0.0981-1.10160.32360.8153-0.3258-0.1651-0.27740.17460.32790.4061-0.0198-0.06740.4403-0.04170.2420.7914-4.40832.2125
119.5754-3.1633.90493.93611.17595.3585-0.00230.20090.06560.0921-0.29770.4971-0.1181-0.7787-0.02290.13830.0270.06250.374-0.1410.4183-36.87528.8852-8.5882
128.9417-0.1446-3.45179.454-0.7452.62770.0482-0.3255-0.73320.4157-0.0375-1.05170.45890.9554-0.03170.26570.0407-0.03880.27590.10470.418910.9034-9.2917-10.459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 209 THROUGH 276 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 277 THROUGH 459 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 460 THROUGH 477 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 205 THROUGH 225 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 226 THROUGH 238 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 239 THROUGH 333 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 334 THROUGH 377 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 378 THROUGH 430 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 431 THROUGH 459 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 460 THROUGH 477 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 141 THROUGH 152 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 141 THROUGH 152 )

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