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- PDB-7vs7: Crystal structure of the ectodomain of OsCERK1 in complex with ch... -

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Basic information

Entry
Database: PDB / ID: 7vs7
TitleCrystal structure of the ectodomain of OsCERK1 in complex with chitin hexamer
ComponentsChitin elicitor receptor kinase 1
KeywordsTRANSFERASE / CERK1 / chitin / PAMP / immunity / symbiosis / immune receptor / ANTIFUNGAL PROTEIN
Function / homology
Function and homology information


transmembrane receptor protein kinase activity / chitin binding / non-specific serine/threonine protein kinase / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
LysM domain receptor kinase CERK1/LYK3-like / 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
Chitin elicitor receptor kinase 1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.015 Å
AuthorsLi, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Integr Plant Biol / Year: 2023
Title: Structural insight into chitin perception by chitin elicitor receptor kinase 1 of Oryza sativa.
Authors: Xu, L. / Wang, J. / Xiao, Y. / Han, Z. / Chai, J.
History
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin elicitor receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9185
Polymers22,9531
Non-polymers2,9654
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint54 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.043, 61.406, 46.409
Angle α, β, γ (deg.)90.000, 113.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitin elicitor receptor kinase 1 / OsCERK1 / LysM domain receptor-like kinase 1 / LysM RLK1 / LysM-containing receptor-like kinase 1 / ...OsCERK1 / LysM domain receptor-like kinase 1 / LysM RLK1 / LysM-containing receptor-like kinase 1 / LysM domain receptor-like kinase 9 / OsLysM-RLK9


Mass: 22953.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: CERK1, RLK9, Os08g0538300, LOC_Os08g42580, P0665C04.34, P0666G10.101
Production host: Insect BA phytoplasma (bacteria)
References: UniProt: A0A0P0XII1, non-specific serine/threonine protein kinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.25M Magnesium chloride, 0.1 M TRIS, pH8.5, and 30% (w/v) PEG4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 15362 / % possible obs: 98.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 31.59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.78
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.319 / Num. unique obs: 1486

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.10-2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EBZ

4ebz


Resolution: 2.015→42.175 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 777 5.06 %
Rwork0.1898 14574 -
obs0.1922 15351 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.5 Å2 / Biso mean: 42.8789 Å2 / Biso min: 20.93 Å2
Refinement stepCycle: final / Resolution: 2.015→42.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 200 38 1753
Biso mean--53.54 39.1 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061770
X-RAY DIFFRACTIONf_angle_d0.9532451
X-RAY DIFFRACTIONf_chiral_restr0.049314
X-RAY DIFFRACTIONf_plane_restr0.005299
X-RAY DIFFRACTIONf_dihedral_angle_d10.2991024
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0151-2.14130.29791140.2253225292
2.1413-2.30660.28151100.2147249199
2.3066-2.53870.27171060.2132246799
2.5387-2.9060.26151450.2216246099
2.906-3.6610.23111600.1964243999
3.661-42.1750.20291420.1603246597
Refinement TLS params.Method: refined / Origin x: 31.3453 Å / Origin y: -2.9306 Å / Origin z: 59.8769 Å
111213212223313233
T0.3393 Å20.0382 Å20.0123 Å2-0.1949 Å2-0.02 Å2--0.218 Å2
L0.8917 °20.2775 °2-0.0333 °2-2.2587 °2-0.6058 °2--2.4814 °2
S-0.0028 Å °-0.0956 Å °0.037 Å °0.0736 Å °0.0067 Å °0.0394 Å °-0.126 Å °-0.0144 Å °-0.0102 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 29 through 233)

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