[English] 日本語
Yorodumi
- PDB-8ay9: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ay9
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, V168A)-ABA-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 / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / 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 / START-like domain superfamily
Similarity search - Domain/homology
Chem-A8S / : / 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: 2.281 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 28, 2024Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03014
Polymers60,2412
Non-polymers78912
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-93 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.763, 62.923, 187.010
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

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Abscisic acid receptor PYL1


Mass: 23269.889 Da / Num. of mol.: 1 / Mutation: V112L, T135L, F137I, T153I, V168A
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: 36971.438 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

-
Non-polymers , 5 types, 56 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 / Abscisic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6 / Details: 30%PEG3350 0.5M CaCl2 Drop 1:1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.281→44.28 Å / Num. obs: 23704 / % possible obs: 95.71 % / Redundancy: 8.6 % / Biso Wilson estimate: 45.07 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1574 / Rrim(I) all: 0.1676 / Net I/σ(I): 7.38
Reflection shellResolution: 2.281→2.362 Å / Redundancy: 1.49 % / Rmerge(I) obs: 0.7724 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 1983 / CC1/2: 0.913 / CC star: 0.977 / Rrim(I) all: 0.8197 / % possible all: 83.74

-
Processing

Software
NameVersionClassification
XDS2018data reduction
XDS2018data scaling
PHENIX1.19.2-4158phasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mn0

5mn0


Resolution: 2.281→44.28 Å / SU ML: 0.3033 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 34.1071
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2596 2077 5.12 %
Rwork0.2025 38528 -
obs0.2055 23704 91.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.22 Å2
Refinement stepCycle: LAST / Resolution: 2.281→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 35 44 3956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793972
X-RAY DIFFRACTIONf_angle_d0.94585377
X-RAY DIFFRACTIONf_chiral_restr0.0546606
X-RAY DIFFRACTIONf_plane_restr0.0062706
X-RAY DIFFRACTIONf_dihedral_angle_d26.5291467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.281-2.330.37131040.30692007X-RAY DIFFRACTION71.13
2.33-2.390.45071330.27932488X-RAY DIFFRACTION87.75
2.39-2.460.29731510.28792574X-RAY DIFFRACTION91.91
2.46-2.530.3951340.27182586X-RAY DIFFRACTION90.1
2.53-2.610.41261350.2682549X-RAY DIFFRACTION92.08
2.61-2.70.30831460.2542520X-RAY DIFFRACTION89.52
2.7-2.810.28721370.24732503X-RAY DIFFRACTION89.52
2.81-2.940.30031290.24222635X-RAY DIFFRACTION93.38
2.94-3.090.35621490.24242651X-RAY DIFFRACTION94.34
3.09-3.290.38251200.24152724X-RAY DIFFRACTION95.53
3.29-3.540.24571470.20412698X-RAY DIFFRACTION95.82
3.54-3.90.25091550.19032639X-RAY DIFFRACTION94.42
3.9-4.460.1761420.1582670X-RAY DIFFRACTION95.13
4.46-5.620.21481260.16012609X-RAY DIFFRACTION92.81
5.62-44.280.21441690.17832675X-RAY DIFFRACTION95.66
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)
10.134573334286-0.597275866338-0.08344905648222.43440717289-0.01314316395520.550377095809-0.324231050477-0.3087084876920.02400327135210.7315320994580.426133492959-0.09944303853490.3500027847960.1051281280930.01757989202211.031903961840.0377606276055-0.1016631349660.8808601809990.06790037009610.6270727468178.402390143817.8112726491355.3763202495
20.8283576495350.6969240516790.3751523248051.9719738329-1.291436653291.653680277970.0293365865441-0.0543065115865-0.01937313452440.452260180823-0.161425867105-0.5793107142690.23580472290.5487265666160.1258096632570.6900020543620.000158127431052-0.1294961989030.5944895778930.1007653300840.5232038306919.443357413664.8211881285745.1523108485
31.561425081640.417876433827-1.04439460781.05937055133-0.645176072282.011901962630.119840580924-0.266240272944-0.003702177798440.209463064203-0.06586723351610.1945313985590.572853092839-0.17978311494-0.02117985798950.74129760346-0.07750209705140.03492051851940.5971151467670.006723791905710.514148763507-7.570781279372.599686690938.1363438979
42.78209660480.981143833077-0.1400615558321.663810753330.6461926456312.689047134980.127970965789-0.08964973045740.02637045820290.651334531853-0.1354063980380.1021204540910.4768759121370.104404222403-0.01130372272550.77642207795-0.0500116115765-0.01699036231430.5068870301250.07789997407830.4367441985610.9505529828844.3796052837942.8953424186
54.50446588754-1.23898309233-1.646459406971.947420090550.8384874064064.316175371890.1049909306280.164210851857-0.4855563623090.12142645116-0.1157949873250.253111523535-0.274724148945-0.07317219535180.0204996939660.612598890058-0.0428649383153-0.09330440848110.3538027731350.1153664849530.4463266008896.569117048437.4923631326941.9236228277
65.73578102739-0.249051666935-2.802283690073.939743525780.2220031016094.235872810460.2079556800440.3153626864520.8387039154490.4244940885160.0691822516846-0.08780423533480.08884674788830.188124440667-0.2312809710280.532098901729-0.0582739474737-0.01473262193420.4753657833580.007930319022630.4208111775152.2764882509313.794926641739.4454912709
70.9212650224950.614321049298-1.37710372761.761738701820.118697211381.980317850410.100358853914-0.1157528094710.26704151420.150527956174-0.132646696211-0.098881025263-0.2050938081780.01139143343340.04922800746940.264790694615-0.0128632152677-0.03746479204090.423778818358-0.02141975736350.453705808339-6.6538245539327.83677279565.81309348707
83.29735315084-0.07296544880340.2176425691651.579197331720.6689335818011.577999780320.03522979596010.2608970438220.925161102445-0.03160886616260.004584435209560.111516935001-0.8153470516990.2551650920210.05875231751330.574915438087-0.07837690922930.01746903360950.5563646874890.009965604139670.61957058314-3.3790816048139.67057561825.27187359931
92.43393483767-0.1096970852950.7606877658361.93622554698-0.3816230143231.97440157626-0.1042641306870.1833364138430.2478303654440.2309191273210.322769952481-0.227538664271-0.471102196535-0.226181553828-0.2202946409630.538343657678-0.05041910279260.04858818998520.501276694956-0.05807968574290.490026631645-5.0938430355137.910827679417.1262193611
102.34402530075-1.1913947959-0.2309515687095.123470991530.3485275291672.46231276776-0.474251350951-0.1674949146120.1325499004590.6711098670730.04795564006551.76965769478-0.21572598221-0.2218797792850.3210515406770.7101242532540.1759188648450.001783821152381.124533813050.01106229363150.971426800243-16.038820626932.48705927827.9707542204
110.627246207909-0.4030492165680.1082993809140.449569009238-0.04393555656061.307355581190.0361601921452-0.03197165602880.09884629856370.10264777494-0.0300017095271-0.0958146296606-0.1535687838420.21857957708-0.001570598734230.38275799248-0.07395154723390.002661260856340.432562981969-0.001870077400450.4099761938046.7137291177625.733991573610.6821412076
121.515012178550.562646601758-0.8388317544351.942524312930.7301710864781.696002109460.04947176838380.2760360897480.149789301593-0.2977535206230.05135516678440.188806375984-0.0372711512616-0.149886642633-0.04723864783850.287853615526-0.032379852425-0.008253212621450.4550922817440.03643898555370.396652630224-2.9879465579221.8170797957-4.26807634763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 181 )
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 207 )
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 219 )
8X-RAY DIFFRACTION8chain 'B' and (resid 220 through 248 )
9X-RAY DIFFRACTION9chain 'B' and (resid 249 through 302 )
10X-RAY DIFFRACTION10chain 'B' and (resid 303 through 322 )
11X-RAY DIFFRACTION11chain 'B' and (resid 323 through 458 )
12X-RAY DIFFRACTION12chain 'B' and (resid 459 through 505 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more