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- PDB-7mwn: An engineered PYL2-based WIN 55,212-2 synthetic cannabinoid senso... -

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Basic information

Entry
Database: PDB / ID: 7mwn
TitleAn engineered PYL2-based WIN 55,212-2 synthetic cannabinoid sensor with a stabilized HAB1 variant
Components
  • Abscisic acid receptor PYL2
  • HAB1-T+
KeywordsPLANT PROTEIN / PYR/PYL/RCAR / PYL2 / HORMONE RECEPTOR / Biosensor / cannabinoid
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 / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Chem-WI5 / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.902 Å
AuthorsPeterson, F.C. / Beltran, J. / Bedewitz, M. / Steiner, P.J. / Cutler, S.R. / Whitehead, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)HR001118C0137 United States
CitationJournal: Nat.Biotechnol. / Year: 2022
Title: Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds.
Authors: Beltran, J. / Steiner, P.J. / Bedewitz, M. / Wei, S. / Peterson, F.C. / Li, Z. / Hughes, B.E. / Hartley, Z. / Robertson, N.R. / Medina-Cucurella, A.V. / Baumer, Z.T. / Leonard, A.C. / Park, ...Authors: Beltran, J. / Steiner, P.J. / Bedewitz, M. / Wei, S. / Peterson, F.C. / Li, Z. / Hughes, B.E. / Hartley, Z. / Robertson, N.R. / Medina-Cucurella, A.V. / Baumer, Z.T. / Leonard, A.C. / Park, S.Y. / Volkman, B.F. / Nusinow, D.A. / Zhong, W. / Wheeldon, I. / Cutler, S.R. / Whitehead, T.A.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYL2
B: HAB1-T+
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,89410
Polymers57,9662
Non-polymers9288
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-29 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.326, 69.226, 142.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Abscisic acid receptor PYL2 / PYR1-like protein 2 / Regulatory components of ABA receptor 14


Mass: 21246.816 Da / Num. of mol.: 1 / Mutation: K64Q,F165A, V166I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL2, RCAR14, At2g26040, T19L18.15 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O80992
#2: Protein HAB1-T+


Mass: 36719.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 7 types, 227 molecules

#3: Chemical ChemComp-WI5 / {(3R)-5-methyl-3-[(morpholin-4-yl)methyl]-2,3-dihydro[1,4]oxazino[2,3,4-hi]indol-6-yl}(naphthalen-1-yl)methanone


Mass: 426.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26N2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM bis-tris propane, 200 mM sodium bromide and 19% (w/v) PEG 3,350
PH range: 6.4-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→46.52 Å / Num. obs: 48429 / % possible obs: 99.6 % / Redundancy: 3.826 % / Biso Wilson estimate: 37.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.066 / Χ2: 0.899 / Net I/σ(I): 11.76 / Num. measured all: 352075 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.953.7721.2781.1625379682367280.5671.48798.6
1.95-23.850.8541.7525727668766830.7460.99299.9
2-2.063.8490.6132.3824817644964470.8570.711100
2.06-2.133.860.5012.9124272629362880.8920.58199.9
2.13-2.23.8690.3893.6923771614761440.9310.451100
2.2-2.273.8720.2814.8722669586258550.9650.32699.9
2.27-2.363.8810.2315.8822244574157320.9730.26899.8
2.36-2.463.8790.1847.2321034543354220.980.21499.8
2.46-2.563.8740.1458.9420414527652690.9860.16999.9
2.56-2.693.8680.11511.0319183496949590.9910.13399.8
2.69-2.843.8680.08813.7418363478047480.9940.10299.3
2.84-3.013.8350.0716.817241451444960.9950.08199.6
3.01-3.223.7970.05421.3615996424142130.9960.06399.3
3.22-3.473.7780.04424.714797394139170.9970.05299.4
3.47-3.83.7340.03828.213490363236130.9970.04599.5
3.8-4.253.7380.03431.112298330132900.9980.0499.7
4.25-4.913.7360.03132.9810699287928640.9980.03799.5
4.91-6.013.7130.03132.669030244524320.9980.03699.5
6.01-8.513.6860.0333.236971190218910.9980.03599.4
8.51-46.523.5730.02734.023680104610300.9990.03198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.43 Å46.52 Å
Translation6.43 Å46.52 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.19.1-4122refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LA7

4la7


Resolution: 1.902→38.61 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 1995 4.12 %
Rwork0.1851 46414 -
obs0.1862 48409 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.72 Å2 / Biso mean: 52.9762 Å2 / Biso min: 28.41 Å2
Refinement stepCycle: final / Resolution: 1.902→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 63 219 3967
Biso mean--46.12 50.2 -
Num. residues----474
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.902-1.950.34411390.3385322498
1.95-20.32051410.28563276100
2-2.060.2721420.25223277100
2.06-2.130.25681390.23353274100
2.13-2.20.24781430.20953303100
2.2-2.290.20151410.19383284100
2.29-2.40.23991410.19343295100
2.4-2.520.21831420.19043288100
2.52-2.680.26031430.20043327100
2.68-2.890.27881420.2083333399
2.89-3.180.20321420.1943330299
3.18-3.640.21261440.1814334099
3.64-4.580.17581460.1501337499
4.58-38.610.18341500.1682351799
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)
12.89970.80551.51367.0845-1.4485.27830.0965-0.6881.56160.39770.03720.0495-1.1511-0.0332-0.15030.5685-0.07790.03450.5821-0.2390.73312.83685.02762.3927
24.91322.6231-5.81081.3999-3.10376.86840.4561-2.73521.04890.2291-0.39970.3283-1.01691.76220.01270.4979-0.11440.00080.7714-0.11360.550128.95931.1104-3.8381
37.54971.457-2.26651.7025-0.47862.3379-0.034-0.18940.09680.0089-0.04730.0137-0.14020.05240.08980.2881-0.0044-0.01330.3538-0.04370.296610.5727-7.1203-2.6212
44.3936-0.64074.37542.2108-1.72738.57850.0309-0.2609-0.4147-0.12330.07820.22920.0501-0.4495-0.08280.265-0.0222-0.00950.32060.01030.372417.4811-21.0138-9.2368
57.1905-6.0892-3.89366.96275.28568.8267-0.1008-0.61160.27560.16890.268-0.26250.04610.1005-0.17720.2285-0.0754-0.02140.4570.03120.294821.3619-13.92890.2571
65.6799-1.4007-5.16913.63112.36417.31320.2132-0.43460.4182-0.260.07450.1425-0.43240.2501-0.34290.288-0.0307-0.04650.2582-0.00840.317813.9298-6.0909-3.3467
77.05040.3112-0.89362.3958-1.47590.9728-0.34290.4573-0.1304-0.1211-0.0436-0.18950.12020.09610.40990.3186-0.0943-0.02240.3977-0.06760.327820.2706-3.6242-8.8138
82.06878.2306-9.09047.8367-6.54628.8452-0.08620.33270.3443-0.1170.11270.0464-0.251-0.2175-0.09250.2960.0397-0.02370.40280.05180.364612.2031-6.9986-12.0464
92.51350.0097-0.13252.14310.72183.1415-0.01850.33330.0667-0.2338-0.27060.4895-0.5422-0.87070.22470.4110.1713-0.07760.5935-0.10360.40983.989-18.0144-41.1406
106.2857-0.263.28682.94150.22265.0612-0.18540.21820.594-0.609-0.1254-0.0161-1.3652-0.02480.25130.77620.0244-0.02830.3587-0.00790.359416.8863-4.364-29.6048
112.4783-1.4617-0.9913.64182.17595.3580.02750.4285-0.1863-0.355-0.18970.062-0.1909-0.190.15940.30810.0409-0.03120.444-0.02550.298715.9094-24.9545-47.8689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 25 )A7 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 33 )A26 - 33
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 55 )A34 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 94 )A56 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 116 )A95 - 116
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 140 )A117 - 140
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 158 )A141 - 158
8X-RAY DIFFRACTION8chain 'A' and (resid 159 through 186 )A159 - 186
9X-RAY DIFFRACTION9chain 'B' and (resid 186 through 368 )B186 - 368
10X-RAY DIFFRACTION10chain 'B' and (resid 369 through 402 )B369 - 402
11X-RAY DIFFRACTION11chain 'B' and (resid 403 through 505 )B403 - 505

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