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- PDB-9tb7: Crystal structure of the CsPYL1(I91L-V112L-V192L)-ABA-HAB1 ternar... -

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Basic information

Entry
Database: PDB / ID: 9tb7
TitleCrystal structure of the CsPYL1(I91L-V112L-V192L)-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: 1.98 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)60,89412
Polymers60,1952
Non-polymers69810
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-77 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.303, 63.053, 187.301
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: 23322.861 Da / Num. of mol.: 1 / Mutation: I91L-V112L-V192L
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, 211 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: 0.1 M Bis-Tris propane, pH 6.5, 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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→93.65 Å / Num. obs: 23693 / % possible obs: 92.2 % / Redundancy: 12.7 % / Biso Wilson estimate: 28.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.051 / Rrim(I) all: 0.183 / Net I/σ(I): 0.795
Reflection shellResolution: 1.98→2.07 Å / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 0.784 / Num. unique obs: 1186 / CC1/2: 0.531 / Rpim(I) all: 0.472

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→93.65 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2504 1152 4.86 %
Rwork0.1897 22538 -
obs0.1927 23690 64.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.05 Å2
Refinement stepCycle: LAST / Resolution: 1.98→93.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 33 201 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783875
X-RAY DIFFRACTIONf_angle_d0.8945244
X-RAY DIFFRACTIONf_chiral_restr0.0537592
X-RAY DIFFRACTIONf_plane_restr0.0066685
X-RAY DIFFRACTIONf_dihedral_angle_d13.65481431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.070.109970.3695117X-RAY DIFFRACTION2.78
2.07-2.180.3587250.2968707X-RAY DIFFRACTION16.25
2.18-2.320.3299720.25371442X-RAY DIFFRACTION33.75
2.32-2.50.33151540.24192866X-RAY DIFFRACTION66.95
2.5-2.750.31892170.23854072X-RAY DIFFRACTION94.24
2.75-3.150.25242080.21074354X-RAY DIFFRACTION99.98
3.15-3.970.23482420.16984384X-RAY DIFFRACTION100
3.97-93.650.21822270.15984596X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 0.439762452243 Å / Origin y: 19.1727729581 Å / Origin z: 22.185798023 Å
111213212223313233
T0.115049199906 Å2-0.0159676003956 Å20.00834855350476 Å2-0.160771361022 Å2-0.0062339049365 Å2--0.177031608326 Å2
L0.404050598073 °20.0213908159419 °2-0.0873739650868 °2-0.590662467631 °2-0.260319252678 °2--1.79842221216 °2
S0.00464604023501 Å °-0.119949422063 Å °0.0385673495244 Å °0.140238670386 Å °-0.0197400588303 Å °-0.0185869720516 Å °-0.0059581703 Å °0.0300410147943 Å °0.00643353545788 Å °
Refinement TLS groupSelection details: all

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