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- PDB-9qk3: X-ray crystal structure of SlPYL1-Coumaric Acid complex -

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Basic information

Entry
Database: PDB / ID: 9qk3
TitleX-ray crystal structure of SlPYL1-Coumaric Acid complex
ComponentsSlPYL1-NIO
KeywordsPLANT PROTEIN / ABA receptor / SlPYL1 / Coumaric Acid
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRivera-Moreno, M. / Merino-Gracia, J. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: Plant Physiol Biochem. / Year: 2025
Title: Natural modulators of abscisic acid Signaling: Insights into polyphenol-based antagonists and their role in ABA receptor regulation.
Authors: Merino, J. / Rivera-Moreno, M. / Bono, M. / Nunez-Villanueva, D. / Gonzalez-Vega, A. / Mayordomo, C. / Infantes, L. / Chikhale, R. / Rodriguez, P.L. / Albert, A.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9813
Polymers25,7381
Non-polymers2422
Water1,22568
1
A: SlPYL1-NIO
hetero molecules

A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9616
Polymers51,4772
Non-polymers4854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3450 Å2
ΔGint4 kcal/mol
Surface area18270 Å2
Unit cell
Length a, b, c (Å)89.869, 89.869, 51.621
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein SlPYL1-NIO


Mass: 25738.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: 101268417 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3Q7HTY9
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 3.5 M ammonium sulfate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→44.93 Å / Num. obs: 26794 / % possible obs: 91.68 % / Redundancy: 1.34 % / Biso Wilson estimate: 31.83 Å2 / CC1/2: 0.766 / Net I/σ(I): 1.32
Reflection shellResolution: 1.65→1.65 Å / Num. unique obs: 1440 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.93 Å / SU ML: 0.2699 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.0482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 1299 4.85 %
Rwork0.2239 25495 -
obs0.225 26794 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 16 68 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451565
X-RAY DIFFRACTIONf_angle_d0.67192128
X-RAY DIFFRACTIONf_chiral_restr0.0499249
X-RAY DIFFRACTIONf_plane_restr0.006279
X-RAY DIFFRACTIONf_dihedral_angle_d13.6196571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.720.44271610.45023041X-RAY DIFFRACTION99.78
1.72-1.790.44161570.41352732X-RAY DIFFRACTION89.89
1.79-1.880.34831710.32882868X-RAY DIFFRACTION98.13
1.89-2.010.27761300.27392479X-RAY DIFFRACTION81.76
2.01-2.160.27930.24682724X-RAY DIFFRACTION86.97
2.16-2.380.26651600.24212756X-RAY DIFFRACTION90.42
2.38-2.720.23941450.24542896X-RAY DIFFRACTION93.17
2.72-3.420.25221300.23213108X-RAY DIFFRACTION99.66
3.46-3.460.20521520.17432891X-RAY DIFFRACTION92.41
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)
10.3098107793170.04506814332240.4575986169150.1238532390370.1835178765820.5797414502740.3671799519570.361644916818-0.1341068682330.584240966715-0.8770080872930.4741334243450.3190686511630.0849898282647-0.0003728344133380.420829866326-6.79998764411E-50.06607963980750.513533833619-0.1539623397660.61704084776233.71893422511.268553633-6.51571670982
20.118815736325-0.285934784090.1025374091960.251667800513-0.3265449541220.431301255654-0.2153500695460.274373687023-0.24133228292-0.3523113992160.317058360616-1.191591374450.3042062687870.6060197499230.000200719035270.4005691527320.02784961550480.03746531315370.549598307254-0.1217234659360.56897247603740.178375083918.3053263058-1.69652235051
30.7645322093480.391981004517-0.2610332273220.3807442225720.2514044029650.598935423087-0.06179909282540.338967367392-0.330706012099-0.002853609000210.181222101632-0.588985513620.120841648880.070460212321-0.0002330622414340.3907211082014.62302930278E-5-0.03934658375380.322955688447-0.06758353436240.45748025707928.657155423810.9208847449-1.59275240772
42.43633569750.9100389335870.0001611863288642.04995542830.104269714170.572398481151-0.0227666131404-0.3895204889970.0477336465410.3133702867090.0598332540264-0.0400670807082-0.00556496012241-0.08693261689749.01413436803E-50.4429674589070.0228054337868-0.03383782511780.372001742844-0.0008108602197240.30122617704823.227182121320.533511560115.7442164942
51.18002257155-1.463468078070.3062759984642.6913499644-0.861486442160.3159208293090.565954161004-0.141522973766-1.02973753847-0.1236879096320.2684593064351.581341528920.544722057206-0.1797674719580.1601599394130.415430708328-0.024121000312-0.04485291791580.4025499221930.06644028039580.55172403272510.060284167913.073956492611.4602195359
60.412319193179-0.4793769747430.2604370329240.9359278085310.1955675276250.5323375713690.158688267274-0.0606101783663-0.7642254485950.3157374726510.0660969230975-0.3465497207210.06656896455840.138112845792-9.8208990069E-50.391423610555-0.00363035419891-0.03957674238130.3284215663970.03191255675540.36997576791327.334635566812.21756232213.2288540436
70.126519915576-0.161275791893-0.1218519245320.1953193852580.08438937011870.372439375310.1534099397080.136149439671-0.639506544736-0.341670256333-0.1030263602871.36081934635-0.183838829024-0.7357174582680.0006473572320710.4016612227230.0261565782364-0.1040846472820.4715665242490.046651097910.66450294487714.60279579716.767020619674.63725959703
80.887607700163-0.6089849463640.5619065519850.391581099015-0.4179066983640.275197457491-0.02656273853220.04199360707880.04627348344020.127909367389-0.027902941021-0.102109973759-0.01541067773250.233375597597-3.59633295603E-60.323927171539-0.0433844225508-0.03623661852840.3597475354990.007791451293610.32107545710936.196872929423.72448001153.46312427191
91.13174400786-0.7630540694050.7030834638470.71243005419-1.032255056221.70772170460.303146300603-0.09226915560270.3294651916980.23690783195-0.3940356340870.734511159088-0.0151332229698-0.0291827111166-0.0005580285142280.308560811041-0.00296510861725-0.01645655994730.296213243579-0.0187938833030.31327225962425.661541286315.1377431966-0.52622717059
101.7842721482-0.2082525130610.4234622460320.926160608961-0.7897811835030.670961626045-0.108602875788-0.0460844695317-0.0353809748093-0.414556542224-0.006184713679210.0590291014772-0.349649821519-0.2125029080340.0001259399676150.3763032859290.0116784707341-0.01922001253350.3397547812610.0245900929570.29368969318221.775061286923.68788147741.76283704492
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 43 )28 - 431 - 16
22chain 'A' and (resid 44 through 57 )44 - 5717 - 30
33chain 'A' and (resid 58 through 75 )58 - 7531 - 48
44chain 'A' and (resid 76 through 114 )76 - 11449 - 87
55chain 'A' and (resid 115 through 127 )115 - 12788 - 100
66chain 'A' and (resid 128 through 149 )128 - 149101 - 122
77chain 'A' and (resid 150 through 157 )150 - 157123 - 130
88chain 'A' and (resid 158 through 170 )158 - 170131 - 143
99chain 'A' and (resid 171 through 189 )171 - 189144 - 162
1010chain 'A' and (resid 190 through 220 )190 - 220163 - 193

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