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- PDB-4ebz: Crystal structure of the ectodomain of a receptor like kinase -

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Basic information

Entry
Database: PDB / ID: 4ebz
TitleCrystal structure of the ectodomain of a receptor like kinase
ComponentsChitin elicitor receptor kinase 1
KeywordsTRANSFERASE / pathogen-associated molecular patterns / Pattern recognition receptors / Chitin Elicitor Receptor Kinase 1 / LysM / lysine motif / chitin oligomer
Function / homology
Function and homology information


response to chitin / cellular response to chitin / chitosan binding / detection of molecule of fungal origin / detection of peptidoglycan / transmembrane receptor protein kinase activity / cellular response to molecule of bacterial origin / cell surface pattern recognition receptor signaling pathway / chitin binding / defense response to fungus ...response to chitin / cellular response to chitin / chitosan binding / detection of molecule of fungal origin / detection of peptidoglycan / transmembrane receptor protein kinase activity / cellular response to molecule of bacterial origin / cell surface pattern recognition receptor signaling pathway / chitin binding / defense response to fungus / kinase activity / 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 / intracellular signal transduction / defense response to bacterium / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
LYK3/4/5 LysM2 domain / LysM domain / LysM domain receptor kinase CERK1/LYK3-like / LysM domain / LysM domain profile. / LysM 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. ...LYK3/4/5 LysM2 domain / LysM domain / LysM domain receptor kinase CERK1/LYK3-like / LysM domain / LysM domain profile. / LysM 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
Chitin elicitor receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsChai, J. / Liu, T. / Han, Z. / She, J / Wang, J.
CitationJournal: Science / Year: 2012
Title: Chitin-induced dimerization activates a plant immune receptor.
Authors: Liu, T. / Liu, Z. / Song, C. / Hu, Y. / Han, Z. / She, J. / Fan, F. / Wang, J. / Jin, C. / Chang, J. / Zhou, J.M. / Chai, J.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Chitin elicitor receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4716
Polymers23,4561
Non-polymers3,0155
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.465, 71.322, 72.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitin elicitor receptor kinase 1


Mass: 23456.076 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CERK1, At3g21630, AT3G21630 / Cell line (production host): sf-21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8R7E6
#2: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate pH6.5, 0.2M sodium acetate and 30% (v/v) PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.792→99 Å / Num. all: 28271 / Num. obs: 28130 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.5 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
DMmodel building
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.792→14.941 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 1414 5.04 %RANDOM
Rwork0.1746 ---
obs0.1762 28060 98.62 %-
all-28453 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.034 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.646 Å2-0 Å20 Å2
2---8.749 Å2-0 Å2
3---12.3949 Å2
Refinement stepCycle: LAST / Resolution: 1.792→14.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 202 301 2049
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint function
X-RAY DIFFRACTIONf_bond_d0.0111801X-RAY DIFFRACTION
X-RAY DIFFRACTIONf_angle_d1.3412440X-RAY DIFFRACTION
X-RAY DIFFRACTIONf_dihedral_angle_d15.734702X-RAY DIFFRACTION
X-RAY DIFFRACTIONf_chiral_restr0.097299X-RAY DIFFRACTION
X-RAY DIFFRACTIONf_plane_restr0.007303X-RAY DIFFRACTION
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7921-1.8560.27471330.2158242892
1.856-1.93020.24371570.18512643100
1.9302-2.01780.20541590.17152649100
2.0178-2.12390.24561530.17962664100
2.1239-2.25660.18551460.16892664100
2.2566-2.43010.21991240.16742703100
2.4301-2.67340.20611430.17392688100
2.6734-3.05740.23151450.17922708100
3.0574-3.84110.16741270.16052755100
3.8411-14.94140.21691270.1808274495
Refinement TLS params.Method: refined / Origin x: 2.5195 Å / Origin y: -10.3461 Å / Origin z: -9.3712 Å
111213212223313233
T0.1499 Å2-0.0032 Å20.0038 Å2-0.1399 Å20.0028 Å2--0.1414 Å2
L1.2729 °2-0.0522 °20.0355 °2-1.2623 °2-0.5569 °2--1.2198 °2
S0.0132 Å °0.0131 Å °0.0753 Å °0.0118 Å °0.016 Å °0.1202 Å °-0.0162 Å °0.033 Å °-0.0195 Å °
Refinement TLS groupSelection details: ALL

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