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- PDB-9h0h: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-OPABACTIN-HAB1 TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 9h0h
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1-OPABACTIN-HAB1 TERNARY COMPLEX
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1 / ABA receptor protein / Opabactin
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / signaling receptor activity / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START-like domain superfamily
Similarity search - Domain/homology
: / : / Abscisic acid receptor PYL1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRivera-Moreno, M. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Mol Plant / Year: 2025
Title: Structural insight into ABA receptor agonists reveals critical features to optimize and design a broad-spectrum activator of ABA signaling.
Authors: Bono, M. / Mayordomo, C. / Coego, A. / Illescas-Miranda, J. / Rivera-Moreno, M. / Infantes, L. / Lopez-Carracedo, P. / Sanchez-Olvera, M. / Martin-Vasquez, C. / Pizzio, G.A. / Merino, J. / ...Authors: Bono, M. / Mayordomo, C. / Coego, A. / Illescas-Miranda, J. / Rivera-Moreno, M. / Infantes, L. / Lopez-Carracedo, P. / Sanchez-Olvera, M. / Martin-Vasquez, C. / Pizzio, G.A. / Merino, J. / Forment, J. / Merilo, E. / Estevez, J.C. / Albert, A. / Rodriguez, P.L.
History
DepositionOct 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 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: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,87511
Polymers60,1672
Non-polymers7089
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-79 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.973, 63.896, 187.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Abscisic acid receptor PYL1


Mass: 23294.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067E666
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 36872.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 444 molecules

#3: Chemical ChemComp-A1IRJ / 1-[2-(3,5-dicyclopropyl-4-ethynyl-phenyl)ethanoylamino]cyclohexane-1-carboxylic acid


Mass: 365.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 0.5M CaCl2, 0.1 M B-T pH 7.0, 25% PEG 3350

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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: Jul 10, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.66→52.83 Å / Num. obs: 581424 / % possible obs: 93 % / Redundancy: 12.9 % / Biso Wilson estimate: 20.83 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.9
Reflection shellResolution: 1.66→1.72 Å / Num. unique obs: 128 / CC1/2: 0.492

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Processing

Software
NameVersionClassification
autoPROCdata scaling
PHASERphasing
PHENIX1.18.2-3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→52.83 Å / SU ML: 0.1488 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.6048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 2284 5.05 %
Rwork0.1909 42900 -
obs0.1926 45183 70.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.61 Å2
Refinement stepCycle: LAST / Resolution: 1.66→52.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 35 435 4209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493858
X-RAY DIFFRACTIONf_angle_d0.69275224
X-RAY DIFFRACTIONf_chiral_restr0.0518584
X-RAY DIFFRACTIONf_plane_restr0.0049683
X-RAY DIFFRACTIONf_dihedral_angle_d21.63991440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.882920.474842X-RAY DIFFRACTION1.11
1.7-1.740.490190.4013173X-RAY DIFFRACTION4.69
1.74-1.780.4129370.3823492X-RAY DIFFRACTION13.48
1.78-1.830.3163710.31851234X-RAY DIFFRACTION33.42
1.83-1.880.3221170.26932087X-RAY DIFFRACTION55.94
1.88-1.940.33481250.28372623X-RAY DIFFRACTION70.03
1.94-2.010.27361610.22393012X-RAY DIFFRACTION80.51
2.01-2.090.22911450.2153222X-RAY DIFFRACTION85.22
2.09-2.190.23771800.19733344X-RAY DIFFRACTION89.53
2.19-2.30.27131780.21983615X-RAY DIFFRACTION96.22
2.3-2.450.252140.2013763X-RAY DIFFRACTION100
2.45-2.640.23072130.20373738X-RAY DIFFRACTION99.97
2.64-2.90.24771800.21143840X-RAY DIFFRACTION99.98
2.9-3.320.2292260.18543781X-RAY DIFFRACTION100
3.32-4.180.19252070.15243880X-RAY DIFFRACTION100
4.18-52.830.17982190.16324054X-RAY DIFFRACTION99.91
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)
13.60923308772-0.516832828852-0.07602997819713.23642257675-0.283320509671.82820674106-0.0636573352491-0.03235618306580.02476971693090.7479491507470.0120430084723-0.3742511450250.1928580348580.3626384980070.0542254509010.3599683657370.0914592725187-0.06218835694910.2175552886280.04227719823970.18634431613110.9301195978.4607907345553.0054411694
22.30000818158-0.6058848443310.4947268147732.16021094041.34419419091.340203339320.121252078016-0.3092035453270.0836084328750.722566021756-0.0618871814225-0.02769610532540.507157403881-0.14200458793-0.0490473933560.4508628135020.0940705951919-0.01557943774150.287307807190.04833156297020.1872146694593.990952813218.0142752545258.6099811662
32.15762927330.442511186932-0.09732281508632.9725830440.2331094011223.63580770684-0.1371612902030.0204637405513-0.1546965094840.293141752243-0.10508573739-0.4943641714550.440233378260.5676254887070.1625332004350.20485981020.07928535746660.004026535298190.2384748202040.0637899568550.1330142670479.221663097334.9518146671445.7572857542
42.28349681496-0.949217021171-1.250035785581.501341838530.8676511616144.376249230060.069923319331-0.2608073535910.1649938092280.08779395815670.006667406909080.460075144967-0.00550471624836-0.1616466248190.0216344567260.15542169717-0.03152556255890.04571742704320.1873030151670.003601047173510.207680611975-9.815529716457.7498466768342.0513103504
51.5497638915-0.480991701871-0.6134037847692.8008733675-1.912892522163.06263445074-0.007228705234020.140682545408-0.2575353294230.03317718886320.2008329481860.4172994399550.549096918222-0.416294195267-0.1355085734060.206125241809-0.06712169884590.001933462112110.1326369511760.0009288810871620.143727364777-6.33850568634-0.43460743548430.817981174
61.82909100899-0.245773099524-0.1619856215532.058588515390.4459576429873.074883840650.0912857397867-0.333633133016-0.02534055170970.30933103330.00908321846590.08204965674150.396571187369-0.1150851484480.0001895578174530.266123736321-0.04883484086830.04313368307280.1448221353760.01249073319770.111163615136-2.84043149988-2.5011330382642.2624784031
73.846134579690.4330918813380.001249744032693.416422992270.3847262090371.31828728549-0.3795745411350.372235036108-0.0604930809067-0.5307295700910.127997292094-0.2021631878370.6224829114760.4435984002030.1437600943160.203144562450.02634828991820.08536492108310.2201915943940.005909321471430.1140325827118.064263717910.52262657349830.6872662537
83.109077814420.104513793868-0.2914390707341.87795166769-0.1649594692831.801518809120.04772073088790.004221933719270.2724529938470.447727562191-0.00679758895945-0.0713431904152-0.0966752441746-0.0706622138764-0.05652366510090.1696467698950.02561222877750.0373075748020.129212515040.02840435299090.05830621972862.586467254218.1078327227947.200731648
92.07429627094-2.22616723665-2.036568958224.202432877810.2728181750894.2714430090.000402106596665-0.3332307707670.3107658291540.1397366113230.0461975503824-0.11993244151-0.4339989368510.079445130432-0.006777241824760.131515372362-0.014966235234-0.02925225598730.136992809546-0.0121194185080.04941958835211.8680174597413.652006471439.7017317796
101.373258113710.121390999545-0.3870469931371.525276171690.3112701699132.514038587220.0919382969579-0.1116773757510.3085482703270.0768983996867-0.02668891417260.103528615794-0.377800915038-0.23479016656-0.02555361332840.07279952518220.01109672592970.01953614204940.101075290629-0.02143956691780.153404881633-5.4618152947931.703642171714.2975643802
110.364514553907-0.255522477896-0.03502664080590.689566242363-0.05790941916682.371054553410.0646308646744-0.03988673937090.07812048126120.0304101804071-0.0121952483722-0.0221496957877-0.1561717560670.160978526619-0.03767194981870.0346883358667-0.04810850792880.01304548105570.1102641446210.004130892588190.1368674877548.4302527245525.177072158310.7712432475
122.333279551070.424101056923-1.066200028362.916110879640.5198723562091.481619116890.06400932112470.4964133526420.108695887882-1.13582264361-0.07469603453010.248678408012-0.0144453788641-0.04461021227420.0587556068315-0.125700490109-0.020265676647-0.001439588444640.1238081862990.04977301156660.0928325734951-2.0493935461221.7393556607-4.17604462057
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 35 )AA22 - 351 - 14
22chain 'A' and (resid 36 through 49 )AA36 - 4915 - 28
33chain 'A' and (resid 50 through 67 )AA50 - 6729 - 46
44chain 'A' and (resid 68 through 90 )AA68 - 9047 - 69
55chain 'A' and (resid 91 through 119 )AA91 - 11970 - 98
66chain 'A' and (resid 120 through 141 )AA120 - 14199 - 120
77chain 'A' and (resid 142 through 149 )AA142 - 149121 - 128
88chain 'A' and (resid 150 through 181 )AA150 - 181129 - 161
99chain 'A' and (resid 182 through 207 )AA182 - 207162 - 187
1010chain 'B' and (resid 186 through 337 )BC186 - 3371 - 124
1111chain 'B' and (resid 338 through 458 )BC338 - 458125 - 245
1212chain 'B' and (resid 459 through 505 )BC459 - 505246 - 293

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