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- PDB-5tzy: GPR40 in complex with AgoPAM AP8 and partial agonist MK-8666 -

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Basic information

Entry
Database: PDB / ID: 5tzy
TitleGPR40 in complex with AgoPAM AP8 and partial agonist MK-8666
ComponentsFree fatty acid receptor 1,Endolysin,Free fatty acid receptor 1
KeywordsFATTY ACID BINDING PROTEIN/HYDROLASE / FFAR1 / partial agonist / FATTY ACID BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


myosin complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / calcium ion binding
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / 7 transmembrane receptor (rhodopsin family) / EF-hand domain / EF-hand domain pair / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-7OS / Chem-MK6 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Myosin regulatory light chain LC-2, mantle muscle / Endolysin
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsLu, J. / Byrne, N. / Patel, S. / Sharma, S. / Soisson, S.M.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40.
Authors: Lu, J. / Byrne, N. / Wang, J. / Bricogne, G. / Brown, F.K. / Chobanian, H.R. / Colletti, S.L. / Di Salvo, J. / Thomas-Fowlkes, B. / Guo, Y. / Hall, D.L. / Hadix, J. / Hastings, N.B. / ...Authors: Lu, J. / Byrne, N. / Wang, J. / Bricogne, G. / Brown, F.K. / Chobanian, H.R. / Colletti, S.L. / Di Salvo, J. / Thomas-Fowlkes, B. / Guo, Y. / Hall, D.L. / Hadix, J. / Hastings, N.B. / Hermes, J.D. / Ho, T. / Howard, A.D. / Josien, H. / Kornienko, M. / Lumb, K.J. / Miller, M.W. / Patel, S.B. / Pio, B. / Plummer, C.W. / Sherborne, B.S. / Sheth, P. / Souza, S. / Tummala, S. / Vonrhein, C. / Webb, M. / Allen, S.J. / Johnston, J.M. / Weinglass, A.B. / Sharma, S. / Soisson, S.M.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6064
Polymers53,1781
Non-polymers1,4283
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.880, 63.950, 90.960
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1 / G-protein coupled receptor 40 / Lysis protein / Lysozyme / Muramidase


Mass: 53178.285 Da / Num. of mol.: 1
Mutation: L42A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R,L42A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R,L42A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: FFAR1, GPR40 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14842, UniProt: P00720, lysozyme
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-MK6 / (5aR,6S,6aS)-3-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy][1,1'-biphenyl]-3-yl}methoxy)-5,5a,6,6a-tetrahydrocyclopropa[4,5]cyclopenta[1,2-c]pyridine-6-carboxylic acid


Mass: 521.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31NO6S
#4: Chemical ChemComp-7OS / (2S,3R)-3-cyclopropyl-3-[(2R)-2-(1-{(1S)-1-[5-fluoro-2-(trifluoromethoxy)phenyl]ethyl}piperidin-4-yl)-3,4-dihydro-2H-1-benzopyran-7-yl]-2-methylpropanoic acid


Mass: 549.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35F4NO4

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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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 22% PEG 400, 0.37M potassium nitrate, 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.22→90.96 Å / Num. obs: 9669 / Biso Wilson estimate: 148.69 Å2
Reflection shellResolution: 3.218→3.234 Å / Redundancy: 6.7 % / CC1/2: 0.539 / % possible all: 84.8

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSSeptember 26, 2012data reduction
autoPROC1.3.0data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZR

5tzr


Resolution: 3.22→90.96 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.794 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.511
RfactorNum. reflection% reflectionSelection details
Rfree0.287 485 5.11 %RANDOM
Rwork0.269 ---
obs0.27 9497 93.3 %-
Displacement parametersBiso mean: 154.91 Å2
Baniso -1Baniso -2Baniso -3
1--30.7179 Å20 Å2-26.5207 Å2
2--9.3664 Å20 Å2
3---21.3515 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: 1 / Resolution: 3.22→90.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 94 0 3017
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123095HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.194255HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d915SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC8
X-RAY DIFFRACTIONt_gen_planes517HARMONIC8
X-RAY DIFFRACTIONt_it3095HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.66
X-RAY DIFFRACTIONt_other_torsion18.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3495SEMIHARMONIC4
LS refinement shellResolution: 3.22→3.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.258 136 5.39 %
Rwork0.274 2389 -
all0.274 2525 -
obs--88.6 %
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)
1-0.01440.3980.78011.49871.68032.7106-0.11540.1831-0.09990.14870.1106-0.1048-0.0678-0.03480.00480.11480.0072-0.1115-0.28470.06060.1601-22.26170.036446.1229
2-0.00340.360.18650-0.13010.00340.0030.0086-0.0111-0.005-0.00650.00790.00680.00480.0035-0.0042-0.00530.0699-0.0068-0.0208-0.0337-13.0103-6.31136.6793
3-0.00270.51740.14750.0004-0.1020.0027-0.00080.0022-0.0205-0.0114-0.00660.0220.0138-0.00370.0075-0.01-0.01290.05120.0002-0.00380.0358-16.49-26.70516.96
40.0530.9641-2.926800.24421.81170.01110.01290.03040.0129-0.01080.0152-0.0261-0.0085-0.00030.0828-0.04050.15550.18280.0637-0.3012-5.899-3.9522-4.7526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|211 A|2214 - A|2278 }
2X-RAY DIFFRACTION2{ A|1002 - A|1012 }
3X-RAY DIFFRACTION3{ A|1022 - A|1054 }
4X-RAY DIFFRACTION4{ A|1062 - A|1161 }

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