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- PDB-4ds8: Complex structure of abscisic acid receptor PYL3-(+)-ABA-HAB1 in ... -

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Basic information

Entry
Database: PDB / ID: 4ds8
TitleComplex structure of abscisic acid receptor PYL3-(+)-ABA-HAB1 in the presence of Mn2+
Components
  • Abscisic acid receptor PYL3
  • Protein phosphatase 2C 16
KeywordsHORMONE RECEPTOR/HYDROLASE / abscisic acid receptor / PP2C / ABA / pyl3 / HORMONE RECEPTOR-HYDROLASE complex
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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 domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / : / Protein phosphatase 2C 16 / Abscisic acid receptor PYL3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsZhang, X. / Zhang, Q. / Wang, G. / Chen, Z.
CitationJournal: Structure / Year: 2012
Title: Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism
Authors: Zhang, X. / Zhang, Q. / Xin, Q. / Yu, L. / Wang, Z. / Wu, W. / Jiang, L. / Wang, G. / Tian, W. / Deng, Z. / Wang, Y. / Liu, Z. / Long, J. / Gong, Z. / Chen, Z.
History
DepositionFeb 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYL3
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9546
Polymers61,4512
Non-polymers5034
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-16 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.745, 69.723, 82.887
Angle α, β, γ (deg.)90.00, 101.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13


Mass: 23323.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g73000, PYL3 / Plasmid: pgex 4t-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) cells / References: UniProt: Q9SSM7
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 38127.586 Da / Num. of mol.: 1 / Fragment: UNP residues 169-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g72770, HAB1 / Plasmid: pgex 4t-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) cells
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 347 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 / Comment: hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 28% PEG3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 22300 / Num. obs: 20350 / % possible obs: 91.26 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Num. unique all: 885 / % possible all: 4.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KLX

3klx


Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.644 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22134 1012 5 %RANDOM
Rwork0.18641 ---
obs0.18815 19318 91.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.779 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å21.58 Å2
2---1.26 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 32 343 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213651
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9534950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32123.197147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85315575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0981526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212730
X-RAY DIFFRACTIONr_mcbond_it0.3041.52337
X-RAY DIFFRACTIONr_mcangle_it0.59523756
X-RAY DIFFRACTIONr_scbond_it1.00831314
X-RAY DIFFRACTIONr_scangle_it1.6484.51194
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 66 -
Rwork0.214 1166 -
obs--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)
110.35457.86752.760320.2928-11.49789.2505-0.40.05080.2451-0.3365-0.0620.04160.26990.65330.46190.4080.02030.07690.29090.030.0841-7.4911.31254.783
24.1699-1.2771-2.727111.51515.47476.9223-0.1955-0.3855-0.07820.20080.07-0.150.16530.71790.12550.09170.0255-0.02980.20380.08110.0499-7.827-14.13253.759
33.2128-0.1464-0.7880.8920.46341.76130.00540.03760.1654-0.04220.0415-0.0554-0.0018-0.1871-0.04690.0743-0.01070.01860.06440.01010.0845-12.358-6.52544.963
40.2361-0.22460.06892.3730.5297-0.31390.04650.3034-0.1433-0.18230.06190.1880.0312-0.1596-0.10830.2615-0.0352-0.03840.33390.03480.2515-16.768-14.80831.594
51.27660.1312-0.43890.8029-1.01040.38910.0153-0.0779-0.1024-0.1725-0.1201-0.08930.12760.08280.10480.1649-0.0301-0.01270.149-0.02770.1087-7.845-17.00728.786
65.7004-3.8031-6.41639.81827.30899.2337-0.1161-0.10190.22520.19720.14690.09870.37120.0053-0.03090.056-0.0345-0.08910.18280.02350.1302-17.222-17.74644.281
70.86680.145-1.63480.73280.74643.7031-0.28780.2575-0.35810.0030.1918-0.28690.3495-0.12150.0960.16540.01270.03210.18-0.02120.2519-3.069-19.6535.628
82.97130.53151.49215.92620.68792.0228-0.1912-0.1925-0.01920.3557-0.37630.740.0754-0.62560.56750.1764-0.048-0.01990.2911-0.05020.252-16.397-6.05650.619
94.7595-1.7922-2.41152.06841.19982.15720.13740.1361-0.0892-0.2058-0.0908-0.0623-0.095-0.0653-0.04660.05890.0012-0.02050.0770.03230.0435-2.521-9.38543.949
107.4436-4.6008-0.79363.7951-0.0137-0.1755-0.1488-0.02730.43270.03280.1252-0.1977-0.02720.01040.02370.1209-0.0257-0.01720.2053-0.00590.1189-8.077-3.17838.057
111.7977-0.89720.2054-0.1830.77880.4896-0.02080.2237-0.11910.01870.0130.02590.1295-0.02840.00770.1653-0.00950.00730.1463-0.030.07071.425-0.1412.812
120.4393-0.02890.06393.2069-0.91610.7380.09980.07360.1309-0.0412-0.15680.0263-0.20170.01530.0570.17990.00250.02230.14930.02170.10661.23917.0364.161
130.670.5262-0.36136.0537-2.17590.9091-0.05850.1239-0.0317-0.11010.0599-0.02550.0998-0.0745-0.00140.0576-0.0129-0.0260.12380.00090.07-3.53210.86910.172
142.68351.6497-2.07443.1255-1.21553.58520.039-0.16970.1296-0.278-0.0669-0.2037-0.34460.27490.02790.169-0.0168-0.01410.137-0.01080.08551.74720.09816.903
152.23270.6887-1.32881.2631-0.09271.9955-0.07180.00810.0488-0.08070.0198-0.02660.0655-0.00310.0520.07790.0102-0.0620.1217-0.01350.05662.3719.15313.9
16-0.65910.0018-0.10822.25760.5835.5703-0.0388-0.092-0.10340.0612-0.2008-0.46270.36331.00470.23960.05050.0144-0.02480.26430.06780.180414.3274.91522.78
170.7316-1.23090.15142.141-0.57071.7001-0.0008-0.02080.0843-0.09330.0142-0.04340.12530.0161-0.01340.1117-0.0289-0.02250.14310.02930.08934.0090.08329.7
181.05940.641-0.45111.3143-0.9662.2778-0.11590.0596-0.0816-0.1837-0.0072-0.30720.16020.34170.12310.07290.02450.020.1278-0.00430.125113.9884.3014.288
1911.8945-4.67460.8905-0.793-2.9414-3.8097-0.80182.1785-0.0407-1.47850.3795-0.27220.5472-1.08970.42231.0564-0.41130.21491.0615-0.23870.26286.2427.633-14.247
201.00240.1615-0.25085.6835-2.40713.5693-0.08940.1764-0.2788-0.7272-0.0356-0.35420.34940.31520.1250.17770.03050.05820.1353-0.06340.10729.476-1.539-0.68
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 31
2X-RAY DIFFRACTION2A32 - 46
3X-RAY DIFFRACTION3A47 - 67
4X-RAY DIFFRACTION4A68 - 98
5X-RAY DIFFRACTION5A99 - 117
6X-RAY DIFFRACTION6A118 - 130
7X-RAY DIFFRACTION7A131 - 144
8X-RAY DIFFRACTION8A145 - 157
9X-RAY DIFFRACTION9A162 - 185
10X-RAY DIFFRACTION10A186 - 207
11X-RAY DIFFRACTION11B185 - 202
12X-RAY DIFFRACTION12B203 - 231
13X-RAY DIFFRACTION13B232 - 265
14X-RAY DIFFRACTION14B266 - 300
15X-RAY DIFFRACTION15B301 - 355
16X-RAY DIFFRACTION16B356 - 376
17X-RAY DIFFRACTION17B377 - 410
18X-RAY DIFFRACTION18B411 - 454
19X-RAY DIFFRACTION19B455 - 470
20X-RAY DIFFRACTION20B471 - 506

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