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- PDB-9tb6: Crystal structure of the MpPYL1-HAB1 complex -

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Basic information

Entry
Database: PDB / ID: 9tb6
TitleCrystal structure of the MpPYL1-HAB1 complex
Components
  • PYL1 receptor from Marchantia polymorpha
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / ABA receptor / inhibitory binary 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
: / 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: 2.39 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

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Assembly

Deposited unit
A: PYL1 receptor from Marchantia polymorpha
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0486
Polymers56,8672
Non-polymers1814
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-40 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.124, 71.515, 103.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PYL1 receptor from Marchantia polymorpha


Mass: 19966.510 Da / Num. of mol.: 1
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: 36900.359 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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium/potassium phosphate, pH 6.5, 20% (w/v) 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: Mar 10, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.39→58.85 Å / Num. obs: 13352 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.979 / Rpim(I) all: 0.128 / Net I/σ(I): 0.692
Reflection shellResolution: 2.39→2.58 Å / Num. unique obs: 569 / CC1/2: 0.636 / Rpim(I) all: 0.901

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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: 2.39→58.85 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 688 5.15 %
Rwork0.1973 --
obs0.2004 13352 64.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→58.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 4 47 3990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084010
X-RAY DIFFRACTIONf_angle_d0.995418
X-RAY DIFFRACTIONf_dihedral_angle_d5.528548
X-RAY DIFFRACTIONf_chiral_restr0.057607
X-RAY DIFFRACTIONf_plane_restr0.009706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.580.4043160.2939318X-RAY DIFFRACTION8
2.58-2.840.3342650.29391383X-RAY DIFFRACTION35
2.84-3.250.31451790.25242901X-RAY DIFFRACTION75
3.25-4.090.26182100.18993934X-RAY DIFFRACTION99
4.09-58.850.2292180.1764128X-RAY DIFFRACTION100

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