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- PDB-8ey0: Structure of an orthogonal PYR1*:HAB1* chemical-induced dimerizat... -

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Basic information

Entry
Database: PDB / ID: 8ey0
TitleStructure of an orthogonal PYR1*:HAB1* chemical-induced dimerization module in complex with mandipropamid
Components
  • Abscisic acid receptor PYR1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / PYR/PYL/RCAR / PYR1 / Hab1 / Hormone receptor / Biosensor
Function / homology
Function and homology information


positive regulation of response to water deprivation / plant-type vacuole membrane / regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase ...positive regulation of response to water deprivation / plant-type vacuole membrane / regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / 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 / START-like domain superfamily
Similarity search - Domain/homology
Chem-3UZ / Abscisic acid receptor PYR1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPark, S.-Y. / Volkman, B.F. / Cutler, S.R. / Peterson, F.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-2128016 United States
National Science Foundation (NSF, United States)2128246 United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity.
Authors: Park, S.Y. / Qiu, J. / Wei, S. / Peterson, F.C. / Beltran, J. / Medina-Cucurella, A.V. / Vaidya, A.S. / Xing, Z. / Volkman, B.F. / Nusinow, D.A. / Whitehead, T.A. / Wheeldon, I. / Cutler, S.R.
History
DepositionOct 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein phosphatase 2C 16
A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1125
Polymers57,5162
Non-polymers5963
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-9 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.405, 92.214, 96.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 36901.273 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 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#2: Protein Abscisic acid receptor PYR1 / ABI1-binding protein 6 / Protein PYRABACTIN RESISTANCE 1 / Regulatory components of ABA receptor 11


Mass: 20614.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O49686
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-3UZ / (2S)-2-(4-chlorophenyl)-N-{2-[3-methoxy-4-(prop-2-yn-1-yloxy)phenyl]ethyl}-2-(prop-2-yn-1-yloxy)ethanamide / Mandipropamid


Mass: 411.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22ClNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.15 mM postassium bromide and 30% PEG 2K-MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21877 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.028 / Rrim(I) all: 0.078 / Net I/σ(I): 26.4
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1126 / CC1/2: 0.782 / Rpim(I) all: 0.326 / Rrim(I) all: 0.909 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.01 Å46.11 Å
Translation4.01 Å46.11 Å

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Processing

Software
NameVersionClassification
PHASER2.6.0phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wvo

4wvo


Resolution: 2.4→30.127 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1920 8.78 %
Rwork0.1719 19957 -
obs0.1774 21877 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.83 Å2 / Biso mean: 63.3957 Å2 / Biso min: 26.71 Å2
Refinement stepCycle: final / Resolution: 2.4→30.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 41 106 3827
Biso mean--62.9 50.26 -
Num. residues----468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.45980.33081070.2454125985
2.4598-2.52630.28841300.2052130690
2.5263-2.60060.25641280.2124132691
2.6006-2.68440.28491360.197138395
2.6844-2.78030.26851370.211138094
2.7803-2.89160.30081320.2038142696
2.8916-3.0230.30821420.2104143397
3.023-3.18230.29161400.1941144699
3.1823-3.38140.23541400.1822144799
3.3814-3.64210.24021360.1737148599
3.6421-4.00780.19271420.15531508100
4.0078-4.5860.20071470.13451486100
4.586-5.77120.19751480.14551531100
5.7712-30.1270.22681550.1736154197
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)
11.50730.3434-0.53053.73430.54725.3390.18110.14910.3771-0.10410.0943-0.2037-0.63840.253-0.23960.34210.04870.05930.32010.00270.544912.844-54.278299.302
27.82352.1272-2.69165.7603-0.42727.22820.1011-0.103-0.26610.0753-0.1478-1.044-0.8120.91980.03150.3664-0.0604-0.08950.3908-0.06670.720123.669-52.924306.908
35.8333-4.5594-1.03953.93521.66922.68150.0871-0.2090.39651.5213-0.0463-0.28970.0558-0.0878-0.11740.5243-0.0391-0.00170.3178-0.00650.49567.949-51.241318.271
42.02310.5345-1.11722.2196-1.0175.48570.02030.0939-0.2671-0.0116-0.1133-0.50480.21150.20620.09720.2540.04680.01140.2710.01380.572419.12-68.053298.733
53.71290.445-2.61751.01130.32164.52890.08280.84140.0414-0.21150.12280.113-0.1294-1.041-0.21810.28320.0283-0.04790.55660.04290.43958.461-64.98283.945
65.7767-1.1255-1.5796.03750.82723.3448-0.2966-1.8776-0.65812.1589-0.0159-0.34571.20360.47050.2861.31410.047-0.06481.08790.29240.63619.225-85.009343.061
77.08630.71711.26191.84-1.04144.88970.258-0.96340.60690.9789-0.3660.1836-0.2931-0.05270.13760.9154-0.09440.05910.4264-0.09510.47770.757-75.188332.829
85.8089-0.2041-3.93463.3211-0.22217.95810.027-0.22930.06220.73280.02150.67340.3503-0.2451-0.04190.572-0.02990.120.26020.02960.6132-6.439-81.107324.542
94.00180.21210.48636.56395.22368.8903-0.0823-1.01690.10111.6471-0.23240.00420.9213-0.1370.28360.8371-0.02240.01450.54360.06370.50913.611-80.882333.996
107.4294-2.279-2.58975.95861.14352.8716-0.0419-0.96990.15861.15510.1029-0.54990.29820.8909-0.06750.7988-0.0335-0.08390.47730.11450.51359.19-79329.368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 186:269 )B186 - 269
2X-RAY DIFFRACTION2( CHAIN B AND RESID 270:302 )B270 - 302
3X-RAY DIFFRACTION3( CHAIN B AND RESID 303:325 )B303 - 325
4X-RAY DIFFRACTION4( CHAIN B AND RESID 326:456 )B326 - 456
5X-RAY DIFFRACTION5( CHAIN B AND RESID 457:510 )B457 - 510
6X-RAY DIFFRACTION6( CHAIN A AND RESID 4:28 )A4 - 28
7X-RAY DIFFRACTION7( CHAIN A AND RESID 29:61 )A29 - 61
8X-RAY DIFFRACTION8( CHAIN A AND RESID 62:112 )A62 - 112
9X-RAY DIFFRACTION9( CHAIN A AND RESID 113:133 )A113 - 133
10X-RAY DIFFRACTION10( CHAIN A AND RESID 134:178 )A134 - 178

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