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- PDB-6kyw: S8-mSRK-S8-SP11 complex -

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Basic information

Entry
Database: PDB / ID: 6kyw
TitleS8-mSRK-S8-SP11 complex
Components
  • Receptor protein kinase SRK8
  • S locus protein 11
KeywordsPLANT PROTEIN / Ligand-receptor complex
Function / homology
Function and homology information


rejection of self pollen / protein serine/threonine kinase activity => GO:0004674 / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / signal transduction / extracellular region / ATP binding
Similarity search - Function
S-locus glycoprotein domain / S-locus receptor kinase, C-terminal / S-locus, receptor kinase / S-receptor-like serine/threonine-protein kinase / S-locus glycoprotein domain / D-mannose binding lectin / PAN-like domain / Domain of unknown function (DUF3403) / Receptor serine/threonine kinase / Plant self-incompatibility response ...S-locus glycoprotein domain / S-locus receptor kinase, C-terminal / S-locus, receptor kinase / S-receptor-like serine/threonine-protein kinase / S-locus glycoprotein domain / D-mannose binding lectin / PAN-like domain / Domain of unknown function (DUF3403) / Receptor serine/threonine kinase / Plant self-incompatibility response / Plant self-incompatibility response (SCRL) protein / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN/Apple domain / Knottin, scorpion toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 serine/threonine-protein kinase / S locus protein 11
Similarity search - Component
Biological speciesBrassica campestris (biennial turnip rape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.60112735603 Å
AuthorsMurase, K. / Hakoshima, T. / Mori, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H06380 Japan
Japan Society for the Promotion of Science15K18683 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism of self/nonself-discrimination in Brassica self-incompatibility.
Authors: Murase, K. / Moriwaki, Y. / Mori, T. / Liu, X. / Masaka, C. / Takada, Y. / Maesaki, R. / Mishima, M. / Fujii, S. / Hirano, Y. / Kawabe, Z. / Nagata, K. / Terada, T. / Suzuki, G. / Watanabe, ...Authors: Murase, K. / Moriwaki, Y. / Mori, T. / Liu, X. / Masaka, C. / Takada, Y. / Maesaki, R. / Mishima, M. / Fujii, S. / Hirano, Y. / Kawabe, Z. / Nagata, K. / Terada, T. / Suzuki, G. / Watanabe, M. / Shimizu, K. / Hakoshima, T. / Takayama, S.
History
DepositionSep 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor protein kinase SRK8
B: Receptor protein kinase SRK8
C: S locus protein 11
D: S locus protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6239
Polymers111,5174
Non-polymers1,1065
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, gel-filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-6 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.562, 143.562, 194.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Receptor protein kinase SRK8


Mass: 50509.461 Da / Num. of mol.: 2
Mutation: P79S, Y80E, I81R, F108V, L110R, L180R, F190S, L214Q, L239S, K248E, V286G, V287A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica campestris (biennial turnip rape)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39276
#2: Protein/peptide S locus protein 11 / S-locus cysteine-rich protein / S-locus pollen protein


Mass: 5249.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Brassica campestris (biennial turnip rape) / References: UniProt: Q9SE17
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 4.91 Å3/Da / Density % sol: 71.44 % / Description: Octahedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15-16% PEG3350, 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 120405 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.7816399259 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.8
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.73 / Num. unique obs: 120405

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.60112735603→43.8355014734 Å / SU ML: 0.33086424461 / Cross valid method: FREE R-VALUE / σ(F): 1.33790816335 / Phase error: 26.2562969258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.250891512589 1999 3.34751155469 %
Rwork0.219900981495 57717 -
obs0.220982051418 59716 94.921396894 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.7030502426 Å2
Refinement stepCycle: LAST / Resolution: 2.60112735603→43.8355014734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 0 184 7006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215315364866994
X-RAY DIFFRACTIONf_angle_d1.167800045889492
X-RAY DIFFRACTIONf_chiral_restr0.05769854419291021
X-RAY DIFFRACTIONf_plane_restr0.006090505788891228
X-RAY DIFFRACTIONf_dihedral_angle_d20.63259266112584
LS refinement shellResolution: 2.6011→2.6662 Å /
RfactorNum. reflection
Rfree0.4107 144
Rwork0.3093 -

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