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- PDB-9tbc: Crystal structure of the MpPYL1(L91I-L111V-L191V-C194L-S198K)-ABA... -

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Basic information

Entry
Database: PDB / ID: 9tbc
TitleCrystal structure of the MpPYL1(L91I-L111V-L191V-C194L-S198K)-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


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 / 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 / : / Uncharacterized protein / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesMarchantia polymorpha (common liverwort)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)58,8906
Polymers58,4812
Non-polymers4104
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-33 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.060, 71.580, 103.640
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: 21423.197 Da / Num. of mol.: 1 / Mutation: L91I,L111V,L191V,C194L,S198K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marchantia polymorpha (common liverwort)
Gene: MARPO_0030s0080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R6X8C9
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37057.551 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 , 4 types, 37 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, pH 7.5, 30% (v/v) 2-Methyl-2,4-pentanediol, 200 mM tri-Sodium citrate

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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: Sep 26, 2025
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→35.79 Å / Num. obs: 23698 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 55.84 Å2 / CC1/2: 0.85 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.39 Å / Num. unique obs: 2565 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.79 Å / SU ML: 0.4964 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 49.8353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3295 1268 5.35 %
Rwork0.261 22430 -
obs0.265 23698 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 22 33 3997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734032
X-RAY DIFFRACTIONf_angle_d0.89895451
X-RAY DIFFRACTIONf_chiral_restr0.0532609
X-RAY DIFFRACTIONf_plane_restr0.0077715
X-RAY DIFFRACTIONf_dihedral_angle_d17.01841507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.68091400.6112425X-RAY DIFFRACTION99.15
2.39-2.50.62061430.54642460X-RAY DIFFRACTION99.54
2.5-2.630.56561260.49662457X-RAY DIFFRACTION99.46
2.63-2.80.50871210.41812488X-RAY DIFFRACTION99.73
2.8-3.010.39711430.33442464X-RAY DIFFRACTION99.69
3.01-3.320.431430.27962485X-RAY DIFFRACTION99.77
3.32-3.80.30871320.22652507X-RAY DIFFRACTION99.51
3.8-4.780.2681570.18692512X-RAY DIFFRACTION99.81
4.78-35.790.23851630.18922632X-RAY DIFFRACTION99.64

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