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- PDB-4mn8: Crystal structure of flg22 in complex with the FLS2 and BAK1 ecto... -

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Basic information

Entry
Database: PDB / ID: 4mn8
TitleCrystal structure of flg22 in complex with the FLS2 and BAK1 ectodomains
Components
  • BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
  • LRR receptor-like serine/threonine-protein kinase FLS2
  • flg22
KeywordsTRANSFERASE/TRANSFERASE RECEPTOR / FLS2 / BAK1 / flg22 / Flagellin / plant immunity / Leucine-rich repeat / TRANSFERASE-TRANSFERASE RECEPTOR complex
Function / homology
Function and homology information


regulation of anion channel activity / defense response by callose deposition in cell wall / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / endomembrane system / detection of bacterium / transmembrane receptor protein tyrosine kinase activity / receptor-mediated endocytosis / receptor protein-tyrosine kinase / defense response ...regulation of anion channel activity / defense response by callose deposition in cell wall / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / endomembrane system / detection of bacterium / transmembrane receptor protein tyrosine kinase activity / receptor-mediated endocytosis / receptor protein-tyrosine kinase / defense response / endosome membrane / non-specific serine/threonine protein kinase / endosome / defense response to bacterium / phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain 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. / Protein kinase domain / 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 / Alpha Beta
Similarity search - Domain/homology
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 / LRR receptor-like serine/threonine-protein kinase FLS2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.062 Å
AuthorsChai, J. / Sun, Y. / Han, Z.
CitationJournal: Science / Year: 2013
Title: Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
Authors: Sun, Y. / Li, L. / Macho, A.P. / Han, Z. / Hu, Z. / Zipfel, C. / Zhou, J.M. / Chai, J.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_asym_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.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LRR receptor-like serine/threonine-protein kinase FLS2
B: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
C: flg22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,38329
Polymers112,4313
Non-polymers3,95226
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-197 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.865, 113.683, 164.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein LRR receptor-like serine/threonine-protein kinase FLS2 / Protein FLAGELLIN-SENSING 2 / Protein FLAGELLIN-SENSITIVE 2


Mass: 85524.281 Da / Num. of mol.: 1 / Fragment: FLS2-LRR UNP RESIDUES 25-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FLS2, At5g46330, MPL12.13, MPL12.8 / Cell (production host): high five / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9FL28, non-specific serine/threonine protein kinase
#2: Protein BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 / AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor ...AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor kinase 3 / AtSERK3 / Somatic embryogenesis receptor-like kinase 3


Mass: 24631.170 Da / Num. of mol.: 1 / Fragment: BAK1-LRR UNP RESIDUES 1-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1, ELG, SERK3, At4g33430, F17M5.190 / Cell (production host): high five / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Protein/peptide / Non-polymers , 2 types, 17 molecules C

#3: Protein/peptide flg22


Mass: 2275.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is synthetic produce
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4

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Sugars , 2 types, 10 molecules

#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.: 1
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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

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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: 4.52 Å3/Da / Density % sol: 72.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M citirc acid pH 4.0, 2.5M ammonium sulfate, 8% (v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jul 12, 2012
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: 3.05→50 Å / Num. all: 38964 / Num. obs: 38653 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.5 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGZ

3rgz


Resolution: 3.062→29.962 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 31.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 1928 5 %
Rwork0.2243 --
obs0.2268 38576 98.81 %
all-38887 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.062→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7253 0 234 0 7487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047633
X-RAY DIFFRACTIONf_angle_d1.02810385
X-RAY DIFFRACTIONf_dihedral_angle_d14.5632808
X-RAY DIFFRACTIONf_chiral_restr0.0781253
X-RAY DIFFRACTIONf_plane_restr0.0041316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0625-3.1390.31231150.305246794
3.139-3.22370.39591330.3087259499
3.2237-3.31850.41051300.3072596100
3.3185-3.42540.37341310.3039260699
3.4254-3.54770.3471420.2714261299
3.5477-3.68950.29371320.21912598100
3.6895-3.85710.2581390.19762618100
3.8571-4.060.22171430.1788263399
4.06-4.31360.22431370.17072610100
4.3136-4.64560.22661360.17112643100
4.6456-5.1110.25361600.1761262099
5.111-5.84580.27191440.2325265299
5.8458-7.34710.29531420.24962697100
7.3471-29.96370.27011440.2482270296
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)
10.2970.1936-0.16390.7442-1.21593.47910.1430.13240.01610.06680.10070.0361-0.03190.0214-0.22990.40420.05180.01260.6752-0.10620.471427.271-9.1053-3.9609
21.4614-1.5424-0.83583.06371.32680.66760.091-0.60410.08871.26780.36890.6256-1.334-0.72130.07041.52430.38350.57171.39980.13640.67217.70777.80350.4369
36.78244.5784-6.44853.1012-4.376.0935-0.4387-0.9945-0.6123-1.4374-0.0308-0.2683.32010.59890.6121.42640.0599-0.07651.08170.00280.735430.2605-25.69656.6544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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