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- PDB-9h0i: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iCB-HAB1 TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 9h0i
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iCB-HAB1 TERNARY COMPLEX
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1 / 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: 1.551 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)60,80010
Polymers60,1672
Non-polymers6338
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-66 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.201, 62.736, 187.143
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, 327 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.: 319 / 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: 41.64 %
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: 1.551→52.11 Å / Num. obs: 650297 / % possible obs: 94.1 % / Redundancy: 12.8 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 1.551→1.607 Å / Num. unique obs: 181 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
autoPROCdata scaling
PHASERphasing
PHENIX1.18.2-3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.551→52.11 Å / SU ML: 0.1299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2129 2469 4.86 %
Rwork0.1743 48297 -
obs0.1762 50766 67.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.77 Å2
Refinement stepCycle: LAST / Resolution: 1.551→52.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 30 319 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113850
X-RAY DIFFRACTIONf_angle_d1.05025211
X-RAY DIFFRACTIONf_chiral_restr0.0727586
X-RAY DIFFRACTIONf_plane_restr0.0066690
X-RAY DIFFRACTIONf_dihedral_angle_d18.89421424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.551-1.580.321820.440847X-RAY DIFFRACTION1.2
1.58-1.610.325970.3818161X-RAY DIFFRACTION4.22
1.61-1.650.3989190.3667375X-RAY DIFFRACTION9.61
1.65-1.680.3657280.3169674X-RAY DIFFRACTION17.11
1.68-1.730.3836470.2669968X-RAY DIFFRACTION24.47
1.73-1.770.3261800.24721324X-RAY DIFFRACTION34.39
1.77-1.820.30841060.22572047X-RAY DIFFRACTION52.33
1.82-1.880.23371350.22342757X-RAY DIFFRACTION69.55
1.88-1.950.24361830.20273783X-RAY DIFFRACTION95.57
1.95-2.030.2242040.18273924X-RAY DIFFRACTION99.98
2.03-2.120.23691930.17183964X-RAY DIFFRACTION100
2.12-2.230.20671970.1663972X-RAY DIFFRACTION100
2.23-2.370.20512110.16723964X-RAY DIFFRACTION100
2.37-2.560.22262150.16963975X-RAY DIFFRACTION100
2.56-2.810.22792170.17553971X-RAY DIFFRACTION100
2.81-3.220.21262250.16824013X-RAY DIFFRACTION100
3.22-4.060.16511870.15164089X-RAY DIFFRACTION100
4.06-52.110.21052130.17714289X-RAY DIFFRACTION99.93
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)
11.035820937360.1110375850460.3875645696911.51065252192-0.2300659993121.022115681060.0101410245065-0.19159343752-0.09169360166350.408956923221-0.00820133986868-0.158829794450.1607078026620.22266379749-0.00770005582530.3757912522930.0328667591657-0.03566509335890.2387934361510.03266647329190.2131364085428.574199364026.6992493278451.4435719439
20.736459486027-0.10515081995-0.1480283147150.534876493976-0.165076220791.271910789070.0343026754992-0.0439945139646-0.06614183068010.1987358433780.04347079921050.204765243550.311419071001-0.176995718828-0.08703681864480.31676656144-0.05431079162610.01991085909510.1544629668110.03761781996490.171009070817-7.64488094092.6384034549738.3948203831
31.447294392120.3282367315970.08065034956881.57286182574-0.3754053069131.430879955170.02919894151160.003412991280030.06431122059490.1592725647740.00485952484797-0.05977827066280.1243104155830.0613547086205-0.02103848879990.2358255694730.0150666029059-0.007519123793170.1356700374190.01264536187660.1220102384482.707346423288.4895607869441.4311363868
41.356340713990.3218057013420.1002634190851.250058444480.01649429104081.832145275420.050614744358-0.004820405526550.199967563370.0318054664053-0.01089239772080.152099384934-0.255048052367-0.0814993397207-0.03343714409450.06595849203370.01186121935230.03482616720770.1033617747860.0049837573760.128986707731-6.4196823922929.03947749216.8377642353
51.8253133795-0.3287514279690.5360413578232.49514570019-0.08334143494561.448598569390.0336270598253-0.1752618218250.3286553982930.2482346648640.1064507642550.295868038463-0.450379768252-0.358339914154-0.03493128416660.2157063108990.04418763041550.06007934105540.169654496311-0.04353523944740.213157309179-9.8793568491436.124060639616.0123958081
61.542976286281.02728468722-0.1093117340712.9146828816-1.351630429012.64243986929-0.0309433366126-0.1891134666710.3854302430090.1070645301480.1736064149150.101679888481-0.506461407253-0.216447297224-0.08555903113590.2929350491470.006777091895160.02467934383910.152446379379-0.06087208272340.206371666198-5.154926283736.936382594221.4317230929
70.615065608183-0.05667907268350.344223837811.039711780530.2066202659260.352711110760.128684416366-0.2563850409690.1696782045410.2372101212880.04204967816010.268933707984-0.19778678148-0.0653837307131-0.09760874097120.162876675948-0.0218718734620.04650637240270.1559846780360.001022773468240.185784489657-5.0704312816328.496800459217.5417703905
80.6536258789390.0833025917743-0.1824172290220.640356055170.006177179217040.8658732929570.0739161694202-0.1715419691180.029106643550.0981606772623-0.0113207091046-0.0736034040704-0.1076979731630.204200979982-0.04103207794060.108911851163-0.03403342990930.018494921660.1466959510230.01409430383930.1435539869698.4720087526328.55314240877.66491207652
90.906059591603-0.9500959711550.02433995438082.55800666406-0.3579208407941.08475576533-0.08873863743980.02781291920090.06991066692890.130129190730.0500690969102-0.255252747649-0.07008203956940.3404191055640.03512090879010.145091134851-0.0375710511475-0.0007204786254450.227214552822-0.02667506961930.16830850888710.791963819821.359867570725.942940222
100.333406397425-0.4829464003350.4400005028291.07807333169-0.07314192460111.531734236960.0258852891864-0.04576088590720.08311067764830.0606732656784-0.0531047559921-0.0854918783076-0.2140500266210.1120476061860.03521336056920.0623166383458-0.05229601458270.01550100618080.1381871806340.01892161338320.1507820854515.0213949903528.084666665110.2416413702
112.66445278065-0.2166749413161.565118776290.85688242676-0.2633432769392.438574562240.1092017318360.202936824378-0.291778751327-0.1091315712480.0237036002189-0.08168778351460.06879975490160.0416744967928-0.1041177193550.0660638631718-0.00749299702380.01923962550250.13089975018-0.001224568452120.1206622266673.1795722179721.1329699628-10.2100270022
122.18755495885-0.271862656055-0.0019208347322.708724650510.1364729976271.482388723220.1125801677240.2742017001690.0531921442773-0.377193650184-0.1231178102270.28727532663-0.0279999263197-0.151083120410.1294726242740.0105926933313-0.01151276075920.008198319587780.1679267239330.002522891712650.137674599231-5.9655948684721.5671754469-6.93675267263
131.26368358292-0.0333477896293-0.243381131381.523774584030.1553884917561.00199581873-0.01757878439410.1264357279010.00208514866277-0.250284025802-0.0197524110953-0.01499660612540.0260741706265-0.006099435986130.1018765802330.03884649335120.0005043370896380.001222137675640.104075619790.01720850720790.1007682489160.069384283097621.61006773-0.684387769427
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 133 )AA68 - 13348 - 113
33chain 'A' and (resid 134 through 207 )AA134 - 207114 - 187
44chain 'B' and (resid 186 through 248 )BC186 - 2481 - 52
55chain 'B' and (resid 249 through 272 )BC249 - 27253 - 76
66chain 'B' and (resid 273 through 316 )BC273 - 31677 - 106
77chain 'B' and (resid 317 through 337 )BC317 - 337107 - 127
88chain 'B' and (resid 338 through 368 )BC338 - 368128 - 158
99chain 'B' and (resid 369 through 402 )BC369 - 402159 - 192
1010chain 'B' and (resid 403 through 439 )BC403 - 439193 - 229
1111chain 'B' and (resid 440 through 458 )BC440 - 458230 - 248
1212chain 'B' and (resid 459 through 487 )BC459 - 487249 - 277
1313chain 'B' and (resid 488 through 505 )BC488 - 505278 - 295

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