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- PDB-6a5e: Crystal structure of plant peptide RALF23 in complex with FER and LLG2 -

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Basic information

Entry
Database: PDB / ID: 6a5e
TitleCrystal structure of plant peptide RALF23 in complex with FER and LLG2
Components
  • GPI-anchored protein LLG2
  • RALF23
  • Receptor-like protein kinase FERONIA
KeywordsTRANSFERASE / a plant receptor-ligand complex FLR
Function / homology
Function and homology information


pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / pollen tube / response to ethylene / response to brassinosteroid / brassinosteroid mediated signaling pathway / stomatal movement / ethylene-activated signaling pathway / root development ...pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / pollen tube / response to ethylene / response to brassinosteroid / brassinosteroid mediated signaling pathway / stomatal movement / ethylene-activated signaling pathway / root development / negative regulation of growth / apoplast / plasmodesma / abscisic acid-activated signaling pathway / defense response to fungus / side of membrane / negative regulation of reactive oxygen species biosynthetic process / transmembrane receptor protein tyrosine kinase activity / post-embryonic development / circadian regulation of gene expression / calcium-mediated signaling / negative regulation of cell growth / hormone activity / cell-cell signaling / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
GPI-anchored protein LORELEI-like / Rapid ALkalinization Factor / Rapid ALkalinization Factor (RALF) / 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. ...GPI-anchored protein LORELEI-like / Rapid ALkalinization Factor / Rapid ALkalinization Factor (RALF) / 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
GPI-anchored protein LLG2 / Rapid alkalinization factor 23 / Receptor-like protein kinase FERONIA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.766 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Receptor-like protein kinase FERONIA
C: GPI-anchored protein LLG2
E: RALF23
F: RALF23
D: GPI-anchored protein LLG2
B: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,62414
Polymers109,0416
Non-polymers2,5828
Water00
1
A: Receptor-like protein kinase FERONIA
C: GPI-anchored protein LLG2
E: RALF23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8127
Polymers54,5213
Non-polymers1,2914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-0 kcal/mol
Surface area21470 Å2
MethodPISA
2
F: RALF23
D: GPI-anchored protein LLG2
B: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8127
Polymers54,5213
Non-polymers1,2914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-1 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.312, 62.360, 97.478
Angle α, β, γ (deg.)105.72, 91.30, 108.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Receptor-like protein kinase FERONIA


Mass: 43363.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FER
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9SCZ4, non-specific serine/threonine protein kinase
#2: Protein GPI-anchored protein LLG2 / LORELEI-like-GPI-anchored protein 2


Mass: 9370.615 Da / Num. of mol.: 2 / Fragment: UNP residues 42-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LLG2, At2g20700
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q6NLF4
#3: Protein/peptide RALF23


Mass: 1786.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant)
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9LUS7*PLUS
#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.: 4
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: 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.: 4
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
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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium malonate, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 32854 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rsym value: 0.096 / Net I/σ(I): 20.89
Reflection shellResolution: 2.76→2.83 Å / Num. unique obs: 3150 / Rsym value: 0.969

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.766→42.607 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.79 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2846 1673 5.09 %
Rwork0.2325 --
obs0.2351 32840 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.766→42.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7396 0 168 0 7564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087676
X-RAY DIFFRACTIONf_angle_d1.29810492
X-RAY DIFFRACTIONf_dihedral_angle_d13.3374504
X-RAY DIFFRACTIONf_chiral_restr0.0751196
X-RAY DIFFRACTIONf_plane_restr0.011342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7662-2.84760.34251390.2822448X-RAY DIFFRACTION90
2.8476-2.93950.39961350.2662650X-RAY DIFFRACTION97
2.9395-3.04450.37081360.28852557X-RAY DIFFRACTION98
3.0445-3.16640.34061260.27682677X-RAY DIFFRACTION97
3.1664-3.31040.36611580.27072612X-RAY DIFFRACTION98
3.3104-3.48490.31251260.25722646X-RAY DIFFRACTION97
3.4849-3.70310.29131530.23252600X-RAY DIFFRACTION98
3.7031-3.98880.25121310.22252589X-RAY DIFFRACTION97
3.9888-4.38990.21661510.19272612X-RAY DIFFRACTION97
4.3899-5.02420.23911540.18592611X-RAY DIFFRACTION97
5.0242-6.32670.29541430.22352561X-RAY DIFFRACTION96
6.3267-42.61210.27791210.24812604X-RAY DIFFRACTION96

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