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- PDB-9tb8: Crystal structure of the CsPYL1 L195C-ABA-HAB1 ternary complex -

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Basic information

Entry
Database: PDB / ID: 9tb8
TitleCrystal structure of the CsPYL1 L195C-ABA-HAB1 ternary complex
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / ABA receptor / inhibitory ternary complex
Function / homology
Function and homology information


protein phosphatase inhibitor complex / regulation of intracellular signal transduction / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / signaling receptor activity / protein homodimerization activity / metal ion binding ...protein phosphatase inhibitor complex / regulation of intracellular signal transduction / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / signaling receptor activity / protein homodimerization activity / metal ion binding / nucleus / 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
Chem-A8S / : / 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: 1.55 Å
AuthorsRivera-Moreno, M. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-153108OB-I00 Spain
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Evolutionary-based remodeling of ABA receptors reveals the structural basis of hormone perception and regulation.
Authors: Rivera-Moreno, M. / Bono, M. / Infantes, L. / Rodriguez, P.L. / Albert, A.
History
DepositionNov 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: 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)60,96215
Polymers60,1572
Non-polymers80513
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-101 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.899, 64.526, 188.220
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: 23284.791 Da / Num. of mol.: 1 / Mutation: L195C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host: Escherichia coli (E. coli) / 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 (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 622 molecules

#3: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 3.57 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7
Details: 0.1 M Bis-Tris propane, pH 7.0, 0.5 M CaCl2, 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: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.55→61.04 Å / Num. obs: 54388 / % possible obs: 93.5 % / Redundancy: 12.8 % / Biso Wilson estimate: 18.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.046 / Rrim(I) all: 0.164 / Net I/σ(I): 0.768
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.725 / Mean I/σ(I) obs: 0.727 / Num. unique obs: 2720 / CC1/2: 0.536 / Rpim(I) all: 0.551

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→61.04 Å / SU ML: 0.1559 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2676 4.92 %
Rwork0.1887 51709 -
obs0.1906 54385 69.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.84 Å2
Refinement stepCycle: LAST / Resolution: 1.55→61.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 36 609 4399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113847
X-RAY DIFFRACTIONf_angle_d1.06775206
X-RAY DIFFRACTIONf_chiral_restr0.0644586
X-RAY DIFFRACTIONf_plane_restr0.0125681
X-RAY DIFFRACTIONf_dihedral_angle_d14.22891419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.5800.321639X-RAY DIFFRACTION0.96
1.58-1.610.2806100.3058132X-RAY DIFFRACTION3.56
1.61-1.640.3324120.2932317X-RAY DIFFRACTION8.16
1.64-1.680.3208260.3042578X-RAY DIFFRACTION14.94
1.68-1.720.3374560.27761099X-RAY DIFFRACTION28.62
1.72-1.760.2773720.27191662X-RAY DIFFRACTION42.23
1.76-1.810.27181230.25832269X-RAY DIFFRACTION58.58
1.81-1.860.32741490.26092936X-RAY DIFFRACTION75.65
1.86-1.920.28291540.2323429X-RAY DIFFRACTION87.6
1.92-1.990.27721930.2083595X-RAY DIFFRACTION92.59
1.99-2.070.26032400.18683811X-RAY DIFFRACTION98.64
2.07-2.170.22881900.18383910X-RAY DIFFRACTION99.98
2.17-2.280.24211920.18793910X-RAY DIFFRACTION100
2.28-2.420.232060.19093942X-RAY DIFFRACTION99.98
2.42-2.610.21812080.18853922X-RAY DIFFRACTION100
2.61-2.870.23562150.19643937X-RAY DIFFRACTION100
2.87-3.290.24142050.18443969X-RAY DIFFRACTION100
3.29-4.140.1912250.15934011X-RAY DIFFRACTION100
4.14-61.040.19292000.17964241X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: 0.84287604621 Å / Origin y: 19.0685464392 Å / Origin z: 22.6897447008 Å
111213212223313233
T0.0982930725532 Å2-0.0582819946887 Å20.000464454212074 Å2-0.113934112971 Å2-0.00327871806243 Å2--0.128916112418 Å2
L0.209122052585 °2-0.0886645061836 °2-0.19413516423 °2-0.381713350175 °2-0.368918888102 °2--1.53472782382 °2
S0.0559492731489 Å °-0.0566948561872 Å °0.0457735491985 Å °0.113357779612 Å °-0.0210835403958 Å °0.00330501111096 Å °-0.105515678166 Å °0.093660268678 Å °-0.0344805012277 Å °
Refinement TLS groupSelection details: all

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