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- PDB-8ay8: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, ... -

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Basic information

Entry
Database: PDB / ID: 8ay8
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, V168A)-iSB9-HAB1 TERNARY COMPLEX
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1_5M / HAB1 / Phosphatase ABA receptor inhibitor complex
Function / homology
Function and homology information


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 / plasma membrane / 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-OE3 / VALINE / Abscisic acid receptor PYL1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsInfantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Sci Adv / Year: 2023
Title: Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought.
Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. ...Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. / Monteiro, A. / Rodriguez, R. / Cruces, J. / Rodriguez, P.L. / Albert, A.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Feb 28, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description

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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: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,42916
Polymers60,3012
Non-polymers1,12714
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-87 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.778, 62.699, 187.327
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 Abscisic acid receptor PYL1


Mass: 23269.889 Da / Num. of mol.: 1
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
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37031.445 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 , 6 types, 252 molecules

#3: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Chemical ChemComp-OE3 / ~{N}-[(1-ethyl-4-methyl-2-oxidanylidene-quinolin-6-yl)methyl]benzenesulfonamide


Mass: 356.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5 / Details: 35% PEG3350 0.5M CaCl2 Drop 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.78→46.83 Å / Num. obs: 91313 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 32.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07953 / Net I/σ(I): 12.87
Reflection shellResolution: 1.784→1.848 Å / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 4445 / CC1/2: 0.463

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDS2019data reduction
XDS2019data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mn0

5mn0


Resolution: 1.78→46.83 Å / SU ML: 0.2896 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 2456 5.06 %
Rwork0.1927 46108 -
obs0.1943 48564 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.09 Å2
Refinement stepCycle: LAST / Resolution: 1.78→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 59 238 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723905
X-RAY DIFFRACTIONf_angle_d0.83015278
X-RAY DIFFRACTIONf_chiral_restr0.0564592
X-RAY DIFFRACTIONf_plane_restr0.008704
X-RAY DIFFRACTIONf_dihedral_angle_d14.49771453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.42261160.46632153X-RAY DIFFRACTION85.95
1.82-1.860.42441460.40642582X-RAY DIFFRACTION100
1.86-1.90.37811430.35042505X-RAY DIFFRACTION100
1.9-1.940.34241330.31752558X-RAY DIFFRACTION99.81
1.94-1.990.27761390.26212497X-RAY DIFFRACTION100
1.99-2.040.3221510.21262585X-RAY DIFFRACTION99.93
2.04-2.10.29251430.232521X-RAY DIFFRACTION99.85
2.1-2.170.27361260.23822580X-RAY DIFFRACTION99.96
2.17-2.250.22991220.21662582X-RAY DIFFRACTION99.89
2.25-2.340.24191490.18572523X-RAY DIFFRACTION99.93
2.34-2.440.22861570.18722540X-RAY DIFFRACTION99.78
2.44-2.570.21791410.18242546X-RAY DIFFRACTION99.89
2.57-2.730.22351170.18662625X-RAY DIFFRACTION99.93
2.73-2.950.22711290.18662620X-RAY DIFFRACTION99.93
2.95-3.240.22361340.18252593X-RAY DIFFRACTION99.82
3.24-3.710.17581260.16682641X-RAY DIFFRACTION99.96
3.71-4.670.20241280.15012667X-RAY DIFFRACTION99.54
4.68-46.830.19591560.18812790X-RAY DIFFRACTION99.46
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)
13.55434754645-2.10569628409-0.5250161028165.022959779790.8383861825241.75432644337-0.122233041755-0.196643380655-0.01473277002640.4794726556630.273361526796-0.5339608111420.148213321420.233556956696-0.1307047250420.505571579640.010500678059-0.06017146648350.3409129271810.01048934419660.35701894719512.56134105386.1415500650551.9071351715
21.9405640553-1.47097885278-0.321986812259.474246446322.650131627963.54947078811-0.276594522698-0.6922458676630.05095284831511.121102711160.1175977790180.2229456751150.3519025775030.138314007806-0.03366471690180.5557185011470.0132686937762-0.01859956524570.5292518522120.07423258128540.2753009858485.216283412347.9736958152958.4252535228
33.439943677190.0635990088596-0.2060918312363.04504439129-0.6734113938962.255136055950.08908061577760.03625228411820.06667592187550.349050108022-0.10724275023-0.1582749071680.3321508331540.0337498019903-0.00916732367350.430297305345-0.0337288886769-0.03889944399730.2699988611280.01815695540740.2011102424761.807161274866.4286999485446.8890756272
41.460054836790.396378728173-0.9348381041684.54791323604-1.613588945643.543798564180.1549908846590.1430802634640.0161881040573-0.3799355890760.06270462310150.5492902158990.332912210615-0.492826792993-0.1165940939850.432032573054-0.02323006782080.01468886936230.331304533560.0275283388140.282364600569-9.183384924996.113736599737.2476165917
51.15801537608-0.6577009420820.3338380266273.86301056873-2.897854997295.171164870620.1214940283590.0508981858607-0.233174630572-0.07317213123870.1806740442230.5503011185580.772884815922-0.506844504964-0.3126053425590.397931091973-0.0563934191429-0.0519524832640.2640288824920.01311614284790.302110959611-7.3751721778-0.17689790454531.0413026837
61.52652508107-0.0599401949996-0.6876839307681.525835879230.6730562506563.076264836930.0707341692987-0.247654658108-0.2129584318280.2982699871290.0456646731030.16148439580.802562474204-0.0930053916927-0.03010448272670.564848533642-0.0767674547438-0.02456762461590.2932883870880.03645258059590.287834803396-3.16151822678-2.6140448071642.1359601796
74.12974501410.430187111786-0.0743141522293.522098636190.3489625265563.95890783203-0.1799454104850.42321948851-0.458412402069-0.356855300423-0.0391671243809-0.1781633621420.2910918597120.0291404372467-0.03189869303360.372579988830.02361260877310.0006310313450.3229547414710.002544074113980.2755611901436.913809420190.81392122689530.0302507072
84.753771029141.06497120827-1.221999657631.59009603598-0.4148418717722.990992135070.192994475434-0.1067623586530.1638850501490.320179635661-0.108992793402-0.02146295971550.23736182768-0.284132104078-0.06081011368320.3857582311410.0137145830835-0.0306434478490.2574024608650.03611866324620.2534706001332.603170871498.2805155664847.1488545612
92.94478086244-2.57753669115-3.550498002134.998586294141.366511772045.826811869160.308505871525-0.2041362186690.5109739436890.0528070238885-0.0144892183758-0.1693903319070.03517494069050.328472952815-0.2566385578110.338251297284-0.0235081212194-0.02336526538590.2918648914650.003908325866290.2220278694491.8625970589513.463497863939.6349160862
109.010278358411.999783162350.3568260180682.000005907912.000080742021.999979645350.485874238860.4377594759330.184897428873-1.47100844803-0.474512512943-0.3768503798590.284498408306-0.625928850922-0.08492199767380.7218864325090.2129676768570.1562373476751.137655420850.4054147942380.408707642156-16.090299271318.248332166150.2546045589
111.64437621131-0.3531975769830.3232705419535.32344058263-3.395721637326.351055442480.0518318334811-0.088480593537-0.07065857113650.269787712615-0.263344372764-0.0544203110868-0.01769826222290.1129588666430.23544866610.133865635952-0.00711402867087-0.01009516296930.235295062351-0.00595089767970.263549115633-6.4374165216918.77779415895.5514786336
122.529146993790.320801848351-0.7033922821084.22588266878-1.652136345832.539285473630.1621883840410.1146934562990.523283339640.04171792245520.02575573422310.364176669765-0.516030412484-0.242292902459-0.1635633399130.2929036081610.04188141594950.03418739515610.266523514613-0.0134672523110.334225342281-6.2419452804334.97628526467.41966086948
133.59622532311-0.519330903911-0.4345610277047.0783606372-1.759982616574.153408869890.086419012366-0.2098099492060.6776653208760.2472660123920.1989683571060.374383866552-0.787008774057-0.236001316847-0.1850853462130.3126586735440.03725114458710.0548919218920.219015187603-0.06197748036570.308261110443-9.8793841696636.054292857316.1341160083
142.805372928434.43604823282-3.338463217839.15480483077-6.701495686196.468781486810.111574712657-0.2794337770980.3681814450560.161796973081-0.0493536181816-0.182763464207-0.6609824252780.283016518006-0.07197283099380.4373127133120.002180382463070.005631916862540.27679949273-0.09234961599020.39753130922-1.0296474093638.78428004118.4229299447
151.73018233339-0.532996284267-1.24930004684.29209937212-2.29475080094.49443831578-0.0942190397505-0.3327094937560.1949111000090.5308950268140.2171298569750.456927450184-0.193082725746-0.355960451055-0.1072428790010.208167544753-0.0453661605968-0.01500031661090.330685076626-0.06139406868540.310268807857-8.2298198732430.088873652821.1525630855
160.650332058238-0.590099605282-0.1935185217890.9026980381170.04410990889863.274987712990.0966908301342-0.1559326501340.04053882029310.02208620814930.0656987445464-0.118947108583-0.08448195085690.386667811156-0.110822521830.255772728226-0.04695895713170.004226242309560.285373320496-0.001839173012120.2799576057028.6288262259528.63263602747.91545734519
171.69443665879-1.117304701730.2252199904176.29882049793-0.9021546234732.12124303002-0.0494386586870.02792359353780.1174039813990.2749835093860.0189270401487-0.672416545918-0.1373176931060.5660488983380.06429116128520.250660510854-0.0203214702406-0.07019254140080.44322375359-0.00980910520930.31652278527214.419574847921.658542242227.2384764605
181.31411040501-1.93352627133-0.06565613479793.50554858078-0.607576155310.750875758214-0.0183357167746-0.0815472249968-0.0474292554291-0.0415323430784-0.06339845555440.112842074143-0.07829899079230.1924728294240.001481316656490.272960774428-0.0278014317171-0.004448151368240.368385831599-0.0007630396030040.2689244823955.7360257269720.6323022224.7748271321
190.468526976227-0.7197493496710.6499670449162.41753594316-2.431026570069.350219550860.0403714921706-0.09141120169340.1934594374090.182830781735-0.0936667727351-0.144818109079-0.3588819622430.4662132975150.0638894372860.29491818357-0.0441378194822-0.00576310003970.283751552696-0.03191203795360.3295765921214.9080329211132.414620949115.527221573
202.1602178718-1.32079453108-0.09628010051514.37353006641-1.997132414222.821692467670.0773220682356-0.04909979877920.0495264391972-0.326153737026-0.133360152255-0.09075199745250.2006325218140.0951382060880.06859736322880.170941852962-0.0138566076726-0.01495109682830.2251594922790.01208934395080.2635757779035.3234816682521.69830605423.01020082796
217.67821334913-0.4057593233313.56090258632.59169616651-0.1946176509337.484105083040.09800652467190.202198600988-0.291236059027-0.249602271553-0.0346157952357-0.3039123073670.0830259865768-0.0537460844264-0.1249963288950.195837191817-0.001687244495570.037454014170.2133657346230.001719949118750.2361898105563.4672528549821.399249092-10.1365553326
223.71721542252-1.980943484350.3195987751737.76133081635-0.1698041869133.372107151260.3162901000050.28667855696-0.0302910836324-0.9578863068-0.1726068523110.596704822012-0.0877326633241-0.239908379129-0.205572493240.18710061154-0.0169530830865-0.01713459239010.3063382486540.004349649093130.24756211943-5.7644701251421.7522127895-6.89074434043
232.539786468361.05898073445-2.767598196963.39805074601-0.6338928551723.39390037565-0.08570774364590.1916451461160.0733025026554-0.1933970076540.1320208511870.1247355445960.0575051576071-0.254051358274-0.07393392683350.110440991734-0.0218029185097-0.05092030040980.229821813259-0.00702797283680.2153705544820.21976226527821.728569078-0.591987763693
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 35 )AA20 - 351 - 16
22chain 'A' and (resid 36 through 49 )AA36 - 4917 - 30
33chain 'A' and (resid 50 through 78 )AA50 - 7831 - 59
44chain 'A' and (resid 79 through 90 )AA79 - 9060 - 71
55chain 'A' and (resid 91 through 119 )AA91 - 11972 - 100
66chain 'A' and (resid 120 through 141 )AA120 - 141101 - 122
77chain 'A' and (resid 142 through 149 )AA142 - 149123 - 130
88chain 'A' and (resid 150 through 181 )AA150 - 181131 - 162
99chain 'A' and (resid 182 through 207 )AA182 - 207163 - 188
1010chain 'A' and (resid 208 through 208 )AB2081
1111chain 'B' and (resid 186 through 203 )BD186 - 2031 - 18
1212chain 'B' and (resid 204 through 248 )BD204 - 24819 - 53
1313chain 'B' and (resid 249 through 272 )BD249 - 27254 - 77
1414chain 'B' and (resid 273 through 302 )BD273 - 30278 - 100
1515chain 'B' and (resid 303 through 337 )BD303 - 337101 - 130
1616chain 'B' and (resid 338 through 368 )BD338 - 368131 - 161
1717chain 'B' and (resid 369 through 387 )BD369 - 387162 - 180
1818chain 'B' and (resid 388 through 402 )BD388 - 402181 - 195
1919chain 'B' and (resid 403 through 423 )BD403 - 423196 - 216
2020chain 'B' and (resid 424 through 439 )BD424 - 439217 - 232
2121chain 'B' and (resid 440 through 458 )BD440 - 458233 - 251
2222chain 'B' and (resid 459 through 487 )BD459 - 487252 - 280
2323chain 'B' and (resid 488 through 505 )BD488 - 505281 - 298

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