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- PDB-9tba: Crystal structure of the CsPYL1 L195C dimer -

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Basic information

Entry
Database: PDB / ID: 9tba
TitleCrystal structure of the CsPYL1 L195C dimer
ComponentsAbscisic acid receptor PYL1
KeywordsPLANT PROTEIN / ABA receptor
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 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: Abscisic acid receptor PYL1


Theoretical massNumber of molelcules
Total (without water)46,5702
Polymers46,5702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.025, 76.281, 81.733
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 22 - 206 / Label seq-ID: 22 - 206

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999970571979, 0.00445372462053, 0.00624656017215), (0.00734715897289, 0.321637498995, 0.946834377542), (0.00220781158773, 0.94685240855, -0.321660756063)Vector: 71. ...NCS oper: (Code: given
Matrix: (-0.999970571979, 0.00445372462053, 0.00624656017215), (0.00734715897289, 0.321637498995, 0.946834377542), (0.00220781158773, 0.94685240855, -0.321660756063)
Vector: 71.6162538615, -12.6442815705, 17.8312556452)

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Components

#1: Protein Abscisic acid receptor PYL1


Mass: 23284.791 Da / Num. of mol.: 2 / 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
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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M (NH4)2SO4, 0.1 M Na cacodylate, pH 6.5, 30% (v/v) PEG 8000

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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: Mar 24, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.47→55.77 Å / Num. obs: 4758 / % possible obs: 83.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 100.36 Å2 / CC1/2: 0.89 / Net I/σ(I): 6.8
Reflection shellResolution: 3.47→3.97 Å / Num. unique obs: 944 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.47→55.77 Å / SU ML: 0.6353 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.1871
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3186 485 10.19 %
Rwork0.2672 4273 -
obs0.2727 4758 83.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.7 Å2
Refinement stepCycle: LAST / Resolution: 3.47→55.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 0 0 2906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242956
X-RAY DIFFRACTIONf_angle_d1.75794018
X-RAY DIFFRACTIONf_chiral_restr0.0864472
X-RAY DIFFRACTIONf_plane_restr0.0123526
X-RAY DIFFRACTIONf_dihedral_angle_d11.5381070
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.541532125055 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.47-3.970.4038980.3357846X-RAY DIFFRACTION51.5
3.97-50.31681870.2671653X-RAY DIFFRACTION97.46
5-55.770.30252000.25251774X-RAY DIFFRACTION99.9

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