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- PDB-9h0j: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1 5M (V112L, T135L, F137I, T1... -

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Basic information

Entry
Database: PDB / ID: 9h0j
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1 5M (V112L, T135L, F137I, T153I, V168A)-iCB-HAB1 TERNARY COMPLEX
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1 5M / ABA receptor protein / iCB
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: 1.96 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)60,77610
Polymers60,1432
Non-polymers6338
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-66 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.245, 62.933, 186.327
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: 23270.875 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, 261 molecules

#3: Chemical ChemComp-A1IRN / ~{N}-[(4-cyano-3-cyclopropyl-phenyl)methyl]-4-methyl-benzenesulfonamide


Mass: 326.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O2S / 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.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 0.5 M 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: 1.96→52.15 Å / Num. obs: 476303 / % possible obs: 97.59 % / Redundancy: 13 % / Biso Wilson estimate: 35.47 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.7
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 3663 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
autoPROCdata scaling
PHASERphasing
PHENIX1.18.2-3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→52.15 Å / SU ML: 0.1953 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4034
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 1804 4.93 %
Rwork0.1741 34786 -
obs0.1758 36590 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.99 Å2
Refinement stepCycle: LAST / Resolution: 1.96→52.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 30 253 4076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00483902
X-RAY DIFFRACTIONf_angle_d0.71185281
X-RAY DIFFRACTIONf_chiral_restr0.0508594
X-RAY DIFFRACTIONf_plane_restr0.0037699
X-RAY DIFFRACTIONf_dihedral_angle_d17.09651455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.27791420.21892667X-RAY DIFFRACTION100
2.01-2.070.23191270.19832694X-RAY DIFFRACTION99.93
2.07-2.140.23921420.18962697X-RAY DIFFRACTION99.89
2.14-2.220.23661350.18622686X-RAY DIFFRACTION99.82
2.22-2.30.21771020.18551889X-RAY DIFFRACTION69.62
2.3-2.410.25181310.17852735X-RAY DIFFRACTION99.76
2.41-2.540.23191580.17532705X-RAY DIFFRACTION99.9
2.54-2.70.21651540.17652694X-RAY DIFFRACTION100
2.7-2.90.20891480.17642728X-RAY DIFFRACTION100
2.9-3.20.22021320.17082749X-RAY DIFFRACTION99.9
3.2-3.660.19991410.15852776X-RAY DIFFRACTION99.9
3.66-4.610.17411370.15252801X-RAY DIFFRACTION100
4.61-52.150.2051550.19142965X-RAY DIFFRACTION99.87
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)
11.05025223533-0.08646694826720.9581820267831.29409932783-0.386189595371.037078809390.0366174296907-0.4110708601480.03288919128480.389497783057-0.0250884911896-0.05993399210740.194462688576-0.02762792364549.21728492556E-50.6417359603690.00491037724219-0.02166443775510.4643015099910.06851161247420.3866301399018.630965082796.7483429749951.1969631292
21.658168637170.115389167661-0.1569628094990.863054250091-0.3625929499840.6150764499820.0356882400256-0.0244059910258-0.0612799131260.1196338525950.07164947422840.233052723990.383129532725-0.210706937056-1.19632297805E-50.558345098816-0.09348669271830.02229903878040.3595723332140.05915805948480.344303325761-7.023031392592.4861246819838.4516672867
31.532213236981.066737774830.7216758960111.5626586601-0.2338020952130.9328956040790.09648272783750.1442804269080.003455686899620.217524733143-0.0885847953811-0.05760777978970.307997201859-0.151668086569-0.0003900269639690.5404032299590.05085840430510.02265277285450.4062075765810.04043861031160.3588366535953.641512412726.865908406142.9158673794
40.4333885008630.4973841473970.1195578296741.59126432748-0.6733529091730.7785289244440.196304753436-0.3509653712590.727462970952-0.06518061969080.120125833811-0.234549950844-0.04928383815260.4006629070210.0001205214983590.480567746583-0.0112925700732-0.006325379820770.4131239265690.009031128607860.3523384954332.1360926178113.858907870639.1719322731
50.7810261529690.707799219238-0.1051179255860.8960221430970.5748683758041.31980336219-0.00408605915619-0.1103220253010.01301987600070.173827993-0.08195458603960.0685629403491-0.0303134949801-0.220705533078-0.0002443577097790.1732626881430.007550403609850.0213790233050.279517205184-0.00446815886970.306486339075-7.7636297025722.36113231345.75173078039
60.538863165687-0.0593806071993-0.2660941355380.21146365975-0.3453967918551.19519702820.189633309891-0.2046505961170.09684979723310.467081749087-0.116956401319-0.0159637505263-0.264224446540.03047780051170.3190888245480.225215944558-0.03276807047680.06955071805090.204569612698-0.03815874296190.287678175054-5.2283895913937.37716949447.50699818532
70.932401203767-0.6862385537230.1834454453010.44040079638-0.1688541636961.531134986050.0621191600255-0.2285031115940.09867270542350.2994158026720.040090986742-0.039694724648-0.363620972146-0.2261620473850.001167064278970.392407301743-0.001003410262520.05382281200030.280477410972-0.08743817820430.301974077418-5.6237340378137.474516062916.9751258618
80.601434077139-0.545569589118-0.01362196523910.5817376963910.2210627676970.470327211905-0.100590668097-0.3968309269450.04697691797940.295305942521-0.03917861839280.119947344123-0.123468653907-0.08372997968860.0001731748449790.370844655074-0.04204150135480.01285273041050.379818960848-0.04374621737930.338008424281-8.2647569287930.340842125320.9808000603
91.25283909771-0.644917466091-0.1326182912260.6128296816280.01453827412530.008459701095230.12711978452-0.3391613137240.08070884019870.110505142876-0.07069264153350.010065103702-0.09475490415750.156525989644-9.23778394852E-50.284130146094-0.07621353924280.01389675985690.3318835590050.002920811381780.3193364731718.4300029017928.63352481897.69044107087
100.6199317351040.03330584706790.5335823054340.366487091354-0.2500215238350.64419717504-0.048481423901-0.0038438739607-0.02313799565070.1162321666990.0461680902081-0.2222234306380.1736359746330.38015931545-0.0001262058382610.381042427962-0.0610649655962-0.01760207231470.4898241196610.00483780524110.39132947093814.399479190321.918087950426.9327942856
110.429458298971-0.7421836847970.2074688286090.912394772361-0.009450821499820.935449309205-0.00242244821871-0.09026704403590.04134382638120.150557908039-0.00800444293847-0.0473901259839-0.07306944458450.1258688496544.96327084216E-50.228154047505-0.07544948138750.007363091453350.2722374050440.008612495302670.2792392931925.191282848126.313298051914.0178871035
120.5250054491990.144417228574-0.2041805511670.1971242605430.2561903454780.4797974451860.1902588619910.122652065405-0.40003693608-0.121593707140.027590778466-0.1861846342590.1396893589470.02856633397940.0004199892984210.2313669379220.01273396451610.03252514664490.2769412669640.003312198919280.288233558873.159327942221.2511199771-10.2071268518
130.4601854660620.3517561418520.4227974560650.3187689217630.3295865055710.4227987405140.08892979663590.0507437722754-0.208279298584-0.4847876048550.06225660505960.4383430265510.134341408045-0.0116533606188-1.54695629282E-50.211949387628-0.0207406160344-0.004541038800660.2840847036260.02240570417550.332393932728-6.0830866579421.6415175299-6.88691648737
141.32468137383-0.1909906328440.01913623391110.7750845515010.4951649127120.280818685772-0.097915104868-0.004023488692350.112788076355-0.05901859422790.00885366405575-0.100750540191-0.0337908607584-0.0423935708528-0.0002525429582570.196391720266-0.01552410158250.002108452136110.2605993149660.02629560378060.2600976400540.033732672397822.1289666201-1.82173983534
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 67 )AA21 - 671 - 47
22chain 'A' and (resid 68 through 141 )AA68 - 14148 - 123
33chain 'A' and (resid 142 through 181 )AA142 - 181124 - 163
44chain 'A' and (resid 182 through 207 )AA182 - 207164 - 189
55chain 'B' and (resid 186 through 212 )BC186 - 2121 - 27
66chain 'B' and (resid 213 through 248 )BC213 - 24828 - 54
77chain 'B' and (resid 249 through 302 )BC249 - 30255 - 101
88chain 'B' and (resid 303 through 337 )BC303 - 337102 - 131
99chain 'B' and (resid 338 through 368 )BC338 - 368132 - 162
1010chain 'B' and (resid 369 through 387 )BC369 - 387163 - 181
1111chain 'B' and (resid 388 through 439 )BC388 - 439182 - 235
1212chain 'B' and (resid 440 through 458 )BC440 - 458236 - 254
1313chain 'B' and (resid 459 through 487 )BC459 - 487255 - 283
1414chain 'B' and (resid 488 through 506 )BC488 - 506284 - 302

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