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- PDB-9gnm: X-ray crystal structure of VvPYL1 -

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Basic information

Entry
Database: PDB / ID: 9gnm
TitleX-ray crystal structure of VvPYL1
ComponentsAbscisic acid receptor PYR1
KeywordsPLANT PROTEIN / VvPYL1 / ABA receptor protein
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRivera-Moreno, M. / Benavente, J.L. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: Physiol.Plantarum / Year: 2024
Title: Chemical activation of ABA signaling in grapevine through the iSB09 and AMF4 ABA receptor agonists enhances water use efficiency.
Authors: Bono, M. / Ferrer-Gallego, R. / Pou, A. / Rivera-Moreno, M. / Benavente, J.L. / Mayordomo, C. / Deis, L. / Carbonell-Bejerano, P. / Pizzio, G.A. / Navarro-Paya, D. / Matus, J.T. / Martinez- ...Authors: Bono, M. / Ferrer-Gallego, R. / Pou, A. / Rivera-Moreno, M. / Benavente, J.L. / Mayordomo, C. / Deis, L. / Carbonell-Bejerano, P. / Pizzio, G.A. / Navarro-Paya, D. / Matus, J.T. / Martinez-Zapater, J.M. / Albert, A. / Intrigliolo, D.S. / Rodriguez, P.L.
History
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYR1
B: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3743
Polymers48,0912
Non-polymers2821
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area18210 Å2
Unit cell
Length a, b, c (Å)54.028, 69.417, 107.698
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 28 through 217)
d_2ens_1(chain "B" and resid 28 through 217)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 28 - 217 / Label seq-ID: 19 - 209

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.820085000928, -0.517833705159, -0.243534073704), (-0.520149507141, -0.851965735049, 0.0599906369572), (-0.238547859923, 0.0774767068444, -0.968035267138)Vector: -1. ...NCS oper: (Code: given
Matrix: (0.820085000928, -0.517833705159, -0.243534073704), (-0.520149507141, -0.851965735049, 0.0599906369572), (-0.238547859923, 0.0774767068444, -0.968035267138)
Vector: -1.91832128933, -4.85509005116, -10.0855454112)

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Components

#1: Protein Abscisic acid receptor PYR1


Mass: 24045.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: VIT_02s0012g01270
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F6HT94
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, pH 5.0, 0.2 M magnesium chloride, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97912 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.1→42.64 Å / Num. obs: 24246 / % possible obs: 99.59 % / Redundancy: 1.34 % / Biso Wilson estimate: 34.49 Å2 / CC1/2: 0.946 / Net I/σ(I): 47.34
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2375 / CC1/2: 0.825 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.64 Å / SU ML: 0.308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2695 1212 5 %
Rwork0.2321 23010 -
obs0.234 24222 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 19 21 3076
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.28573697156 Å
LS refinement shellResolution: 2.1→2.18 Å / % reflection obs: 98.48 %
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)
10.5153485959730.2003317595820.01216150877040.4721541138580.3076121937580.0852838742021-0.0373646933288-0.0313142699794-0.0243289707613-0.09180909491760.09932063123310.042253776225-0.0789892957531-0.0285880561691-6.79017447965E-60.4037620978180.01048470321460.0136574763840.3042217359360.01073573220470.352475419247-3.72938920326-7.85656833461-24.7256569091
20.5715823625320.0605570388608-0.6375499979090.0917627435458-0.2701721692390.4348811825720.0319688462805-0.1451627251640.06859174330140.332806082641-0.0119069884355-0.158381122395-0.9543454792180.3951801766620.003790279176970.418834245351-0.0258101636089-0.002390305205760.423858836740.009924085200870.35023937896611.53059183687.57730712647-17.4751201259
30.7246771475950.336868137299-0.1294966158031.439662605370.2200724847980.674198358012-0.04881837658990.147031821122-0.09325248353560.03662812962440.04007451255840.00033473453904-0.1320149980470.147470695539-8.93667574821E-50.2788660486750.004966570282160.01797706320230.2993977656270.04464674844530.2858882185533.33556964565-2.78864565513-22.6055124243
40.483051798053-0.1312275619960.1139279541430.0877986760687-0.2385730702220.507078843693-0.0133400752263-0.41360297392-0.2862353415210.2720147770830.2440055895590.4786887851440.0586442537473-0.09704389627968.02541767811E-50.367341419267-0.04121732493910.02406392072230.2986827229420.04343842899850.356292902475-0.189545911824-2.9273121545-12.0588820127
50.3908835475590.0118593478380.0697641565934-0.0570449918566-0.2158729853250.2722912222430.11394193784-0.4972164120550.3307854292750.490858837556-0.08605793132790.190053692595-0.21638168325-0.0190908069228-0.0001791380626230.63137322294-0.003652073662940.003751636841710.360722180027-0.07150791103490.4782210705945.900185461316.8909077416416.4493826122
60.187710562254-0.01925258306160.194301364733-0.243687937665-0.1561012214220.2049843248910.034091758481-0.1293758335430.0379889322903-0.151722766659-0.05338290367650.0323505779151-0.1794027401340.0733174118171-0.0002445662208760.331891612909-0.0194399731097-0.03712506022080.385769404222-0.02468064205480.3655778724894.43112908981-2.3925872803611.2972787252
70.0697006991666-0.07415210824710.0262388223761-0.00536047171192-0.07343837719020.03660410027020.2311981734610.1427685581510.00873694995305-0.1545828216850.05378264058330.5962488361820.474714293276-0.103718744668-0.0001718734996820.475838218802-0.108464086479-0.03014687128120.375042704260.045673167140.436210076662.49904294953-14.41634444134.30460247666
80.267104322061-0.03840518109910.1169085779120.08413996821860.05802720307830.08425582258610.02290840353230.0422212417107-0.204536758754-0.1939016395190.2936344584330.2492998647170.615777760669-0.5299758117240.0009441996469130.6153966951760.0408632918749-0.002221635219930.3596054468590.02342492838090.4669579646697.41341009845-22.80966607339.53441230101
90.6295570301440.1193139705040.4800346745870.0703248251818-0.02802328416110.4918035618560.1017218935840.0620729703105-0.03314344696570.331748676104-0.1982717206590.07597828195760.5964065824180.0752577615548-0.006701980165350.4860902248070.0340070547365-0.02545789933870.3621599141170.01671193951550.35020664425510.4745800979-14.32224853978.55844508639
100.7264059793770.3109524619160.5611582363410.90121100412-0.2188882662290.9341834987680.0229576054868-0.3056804758570.1629838990660.156114440536-0.0180171424583-0.04028533555720.106958982930.122701336518-6.82002436151E-50.278682982955-0.02764484904590.005301143427940.35879342687-0.02106434067090.3329480529087.63960767469-1.972186922189.19015627591
110.409482568361-0.19994417744-0.0152490308976-0.07913182160140.02055138896930.1966187500360.3025024259390.1182755388290.2280458044550.0791892404394-0.1794287525830.0596174332772-0.1193617388260.0577557489078-0.000192103934010.423851031375-0.0120749402781-0.010402185590.372301296540.02677934191040.3211470814993.31249363687-2.476534880491.50807899752
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 86 )AA28 - 861 - 59
22chain 'A' and (resid 87 through 127 )AA87 - 12760 - 100
33chain 'A' and (resid 128 through 189 )AA128 - 189101 - 162
44chain 'A' and (resid 190 through 219 )AA190 - 219163 - 192
55chain 'B' and (resid 28 through 57 )BB28 - 571 - 30
66chain 'B' and (resid 58 through 86 )BB58 - 8631 - 59
77chain 'B' and (resid 87 through 98 )BB87 - 9860 - 71
88chain 'B' and (resid 99 through 114 )BB99 - 11472 - 87
99chain 'B' and (resid 115 through 149 )BB115 - 14988 - 122
1010chain 'B' and (resid 150 through 189 )BB150 - 189123 - 162
1111chain 'B' and (resid 190 through 217 )BB190 - 217163 - 190

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