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- PDB-9tb5: Crystal structure of the MpPYL1-ABA-HAB1 ternary complex -

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Basic information

Entry
Database: PDB / ID: 9tb5
TitleCrystal structure of the MpPYL1-ABA-HAB1 ternary complex
Components
  • MpPYL1 receptor
  • 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: 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: MpPYL1 receptor
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8666
Polymers58,4572
Non-polymers4104
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-33 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.060, 71.997, 103.546
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 MpPYL1 receptor


Mass: 21399.133 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: 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, 51 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.: 47 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M magnesium formate, pH 5.9, 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: Sep 21, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.98→45.18 Å / Num. obs: 37271 / % possible obs: 99.71 % / Redundancy: 9.8 % / Biso Wilson estimate: 52.73 Å2 / CC1/2: 0.923 / Net I/av σ(I): 7.5 / Net I/σ(I): 0.654
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 2502 / CC1/2: 0.438

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→45.18 Å / SU ML: 0.4415 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.9419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2914 1813 5.19 %
Rwork0.2263 33124 -
obs0.2297 34937 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.01 Å2
Refinement stepCycle: LAST / Resolution: 1.98→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 22 47 4008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754029
X-RAY DIFFRACTIONf_angle_d0.86185447
X-RAY DIFFRACTIONf_chiral_restr0.0539608
X-RAY DIFFRACTIONf_plane_restr0.0099715
X-RAY DIFFRACTIONf_dihedral_angle_d15.8231505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.6049590.6371160X-RAY DIFFRACTION43.38
2.03-2.090.49141210.52962323X-RAY DIFFRACTION86.03
2.09-2.160.46251090.49062448X-RAY DIFFRACTION91.62
2.16-2.240.44041320.41772685X-RAY DIFFRACTION99.19
2.24-2.330.40191380.37112711X-RAY DIFFRACTION99.86
2.33-2.430.40591550.3492645X-RAY DIFFRACTION99.93
2.43-2.560.36241430.32052689X-RAY DIFFRACTION100
2.56-2.720.35781570.29842720X-RAY DIFFRACTION99.9
2.72-2.930.3221620.26292667X-RAY DIFFRACTION99.89
2.93-3.230.28851690.23132707X-RAY DIFFRACTION99.83
3.23-3.690.28891720.21022706X-RAY DIFFRACTION99.76
3.69-4.650.25871370.16922775X-RAY DIFFRACTION99.97
4.65-45.180.24041590.17252888X-RAY DIFFRACTION99.77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.512508768391.500931329621.536933121424.134728035391.27177132023.259910001690.1890372194270.494724080448-0.5175196405820.4894123844980.3834879446140.0356219975820.894731895911-0.00808152480615-0.6271687822110.8709582292250.101314681105-0.04939819004010.6026701795710.0780164615340.958553939238-49.494029571310.2459388786-6.30838935743
23.84949818261-0.5643007221330.04113170666361.800555903630.145069869064.679132026870.1547290738010.3422159277740.382153442392-0.2584880443680.1780107928960.4834911064830.0340103393677-0.656100935483-0.2580317454670.5347312306890.039197263272-0.07199401401050.4495043494430.02001809079210.665797863304-35.68756899288.80344901881-1.31752380585
35.10627704515-0.8981531529040.8182868717345.02202580177-1.721421539974.27610201376-0.189674310404-0.729471446245-0.4198703329061.244277960330.1130834577090.236348510501-0.435645905529-0.696943721540.05900183964080.595916914459-0.02243088392170.06086354572560.542089028313-5.41103201467E-50.404448193242-28.820098420514.454024262312.7038896341
45.62971351823-2.48366572441-0.7823899851886.854898504670.06374066707873.97960323664-0.244580796843-0.9597083725120.2636813976850.7009342016350.310639112181-0.6114908058360.181652751640.398623574417-0.02484467010820.4462396042990.03558012391480.005047373228570.526837448135-0.002904619636080.558982999784-18.435923336711.30146426069.24991929211
51.28373905397-0.0233783902841.043933303210.7835329965320.3700918149531.91632830253-0.145470797982-0.0744741251184-0.00541671810758-0.0647278132907-0.04317962697130.000833715721079-0.2239970751740.06680079190160.169676864070.492336055658-0.040450355188-0.0578467811380.456265355725-0.06084266324570.811612251293-28.714891941217.11602622492.45854767744
67.323268456672.17205825595-1.893968701983.05152400022-1.799287295454.45336489635-0.7451355955240.0949615780187-0.420036115619-0.3636538520480.3056809088330.4364158746950.520886430596-0.8315735745440.3763124060410.663017801524-0.0233073545862-0.09115893629070.679070146378-0.0948032314870.681209594524-44.69938729264.373837352280.918506991437
72.17800064703-0.255096792693-0.03564376578241.969520396120.3745905367152.96895397567-0.0184356990093-0.07910904157-0.272379959988-0.0436217586397-0.0494982911233-0.1793842686780.4248829451560.2660790161080.008036316531210.4512437811440.0109380748531-0.04211865961870.434673551624-0.02045893394230.667546985138-28.42668616794.26881818947-0.962748093248
81.272543558330.638077280338-0.3622643952033.43873042540.8277127350622.12872730808-0.0222288849480.0547062118505-0.2939190403340.560008111053-0.1158318473890.3249347355470.3002487245170.2370980542990.1123559318650.4538101567170.0236954130881-0.01080144814120.4029471172180.02126203229220.531122688595-0.667134825988-18.386263533520.9351895467
92.15194444333-2.00927427823-0.03754473768444.2285699720.7630705884631.501340680640.06807969295780.027616892303-0.375102299118-0.086392433748-0.0437623823480.735718926240.452303335283-0.2487580456150.001767933062870.593815404265-0.0525272218239-0.09771549150470.4601467103220.04388444894910.67309639139-13.1863727644-23.169989034316.9270371803
102.19474378901-1.073202992620.8930427487783.06292686309-0.9150884322992.035975190860.2570509563870.33587780084-0.0996219675319-0.215599212525-0.213889759284-0.1871331539030.1916751018410.528026556872-0.05858037939050.5069530429110.0445359706187-0.004181400331260.497584271821-0.03959116329630.532623033931-0.155121449628-8.8961117561111.2937714265
112.651943565430.494154556094-0.786176633641.498474219570.3682677060972.43486422737-0.0247526332085-0.107429466233-0.1751976251680.14437894411-0.0547898071841-0.1046607700220.06553325808140.6884129342070.06521000489110.546002804103-0.0422585994816-0.08298373270720.5696233395920.06567990811920.74058635046311.1512611477-6.2465408034421.7020564774
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 34 through 49 )AA34 - 493 - 18
22chain 'A' and (resid 50 through 78 )AA50 - 7819 - 47
33chain 'A' and (resid 79 through 105 )AA79 - 10548 - 74
44chain 'A' and (resid 106 through 118 )AA106 - 11875 - 87
55chain 'A' and (resid 119 through 148 )AA119 - 14888 - 117
66chain 'A' and (resid 149 through 163 )AA149 - 163118 - 132
77chain 'A' and (resid 164 through 206 )AA164 - 206133 - 175
88chain 'B' and (resid 180 through 248 )BC180 - 2481 - 69
99chain 'B' and (resid 249 through 315 )BC249 - 31570 - 133
1010chain 'B' and (resid 316 through 487 )BC316 - 487134 - 305
1111chain 'B' and (resid 488 through 511 )BC488 - 511306 - 329

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