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- PDB-6a5b: Crystal structure of plant Receptor-like Kinase FER -

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Basic information

Entry
Database: PDB / ID: 6a5b
TitleCrystal structure of plant Receptor-like Kinase FER
ComponentsReceptor-like protein kinase FERONIA
KeywordsTRANSFERASE / a plant receptor F
Function / homology
Function and homology information


pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to brassinosteroid / response to ethylene / brassinosteroid mediated signaling pathway / ethylene-activated signaling pathway / stomatal movement / root development / plasmodesma ...pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to brassinosteroid / response to ethylene / brassinosteroid mediated signaling pathway / ethylene-activated signaling pathway / stomatal movement / root development / plasmodesma / abscisic acid-activated signaling pathway / defense response to fungus / transmembrane receptor protein tyrosine kinase activity / post-embryonic development / circadian regulation of gene expression / negative regulation of cell growth / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-like protein kinase FERONIA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 Å
AuthorsXiao, Y. / Chai, J.
CitationJournal: Nature / Year: 2019
Title: Mechanisms of RALF peptide perception by a heterotypic receptor complex.
Authors: Xiao, Y. / Stegmann, M. / Han, Z. / DeFalco, T.A. / Parys, K. / Xu, L. / Belkhadir, Y. / Zipfel, C. / Chai, J.
History
DepositionJun 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-like protein kinase FERONIA


Theoretical massNumber of molelcules
Total (without water)46,8161
Polymers46,8161
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16260 Å2
Unit cell
Length a, b, c (Å)60.545, 63.509, 107.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-like protein kinase FERONIA / Protein SIRENE


Mass: 46815.863 Da / Num. of mol.: 1 / Fragment: UNP residues 21-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FER, AAK1, SIR, SRN, At3g51550, F26O13.190
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9SCZ4, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris pH 6.5, 25%(w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21471 / % possible obs: 98.2 % / Redundancy: 7 % / Rsym value: 0.075 / Net I/σ(I): 20.4
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 2099 / Rsym value: 0.642

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Processing

Software
NameVersionClassification
REFMAC(1.10.1_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5C

6a5c


Resolution: 2.205→40.595 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1102 5.13 %
Rwork0.1915 --
obs0.1937 21469 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.27 Å2 / Biso mean: 42.9336 Å2 / Biso min: 22.39 Å2
Refinement stepCycle: final / Resolution: 2.205→40.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 0 86 3010
Biso mean---45.73 -
Num. residues----376

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