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- PDB-5gr8: Crystal structure of PEPR1-AtPEP1 -

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Basic information

Entry
Database: PDB / ID: 5gr8
TitleCrystal structure of PEPR1-AtPEP1
Components
  • Elicitor peptide 1
  • Leucine-rich repeat receptor-like protein kinase PEPR1
KeywordsTRANSFERASE / PEPR1 / DAMP / PRR / AtPEP1.
Function / homology
Function and homology information


peptide receptor activity / response to ethylene / protein serine/threonine kinase activity => GO:0004674 / response to jasmonic acid / guanylate cyclase activity / plasmodesma / response to wounding / membrane => GO:0016020 / non-specific serine/threonine protein kinase / immune response ...peptide receptor activity / response to ethylene / protein serine/threonine kinase activity => GO:0004674 / response to jasmonic acid / guanylate cyclase activity / plasmodesma / response to wounding / membrane => GO:0016020 / non-specific serine/threonine protein kinase / immune response / innate immune response / protein serine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Elicitor peptide / Elicitor peptide 1-7 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...Elicitor peptide / Elicitor peptide 1-7 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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
Similarity search - Domain/homology
Elicitor peptide 1 / Leucine-rich repeat receptor-like protein kinase PEPR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsChai, J.J. / Tang, J.
CitationJournal: Cell Res. / Year: 2015
Title: Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1
Authors: Tang, J. / Han, Z.F. / Sun, Y.D. / Zhang, H.Q. / Gong, X.Q. / Chai, J.J.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 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: Leucine-rich repeat receptor-like protein kinase PEPR1
D: Leucine-rich repeat receptor-like protein kinase PEPR1
J: Elicitor peptide 1
P: Elicitor peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,44415
Polymers157,5274
Non-polymers2,91811
Water1,18966
1
A: Leucine-rich repeat receptor-like protein kinase PEPR1
J: Elicitor peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1698
Polymers78,7632
Non-polymers1,4056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint10 kcal/mol
Surface area28970 Å2
MethodPISA
2
D: Leucine-rich repeat receptor-like protein kinase PEPR1
P: Elicitor peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2767
Polymers78,7632
Non-polymers1,5125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint25 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.490, 96.967, 106.013
Angle α, β, γ (deg.)90.00, 110.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ADJP

#1: Protein Leucine-rich repeat receptor-like protein kinase PEPR1 / PEPR1


Mass: 76864.180 Da / Num. of mol.: 2 / Fragment: UNP residues 29-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PEPR1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9SSL9, non-specific serine/threonine protein kinase
#2: Protein/peptide Elicitor peptide 1 / AtPEP1


Mass: 1899.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LV87

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Sugars , 2 types, 10 molecules

#3: 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: obtained synthetically
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
#4: 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.: 7 / Source method: obtained synthetically / 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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Non-polymers , 2 types, 67 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v Polyethylene Glycol Monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.587→50 Å / Num. obs: 58543 / % possible obs: 89.7 % / Redundancy: 5.9 % / Net I/σ(I): 43
Reflection shellResolution: 2.59→2.63 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MN8

4mn8


Resolution: 2.587→49.553 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 2967 5.07 %
Rwork0.2345 --
obs0.2372 58489 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.587→49.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11065 0 187 66 11318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911494
X-RAY DIFFRACTIONf_angle_d1.61615594
X-RAY DIFFRACTIONf_dihedral_angle_d16.4124337
X-RAY DIFFRACTIONf_chiral_restr0.1181843
X-RAY DIFFRACTIONf_plane_restr0.0082020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5874-2.62980.36271380.29272430X-RAY DIFFRACTION91
2.6298-2.67510.34171520.26682599X-RAY DIFFRACTION100
2.6751-2.72380.39391390.26032674X-RAY DIFFRACTION100
2.7238-2.77620.39241340.24652669X-RAY DIFFRACTION100
2.7762-2.83280.32861260.24392637X-RAY DIFFRACTION100
2.8328-2.89440.36131240.23242646X-RAY DIFFRACTION100
2.8944-2.96170.30251400.23652659X-RAY DIFFRACTION100
2.9617-3.03580.27591630.23652657X-RAY DIFFRACTION100
3.0358-3.11790.36091360.24712653X-RAY DIFFRACTION100
3.1179-3.20960.31631380.24462659X-RAY DIFFRACTION100
3.2096-3.31320.32441430.24992654X-RAY DIFFRACTION100
3.3132-3.43160.32841350.2512658X-RAY DIFFRACTION100
3.4316-3.56890.32741460.24142653X-RAY DIFFRACTION100
3.5689-3.73130.29271540.23132625X-RAY DIFFRACTION100
3.7313-3.9280.2971420.22642650X-RAY DIFFRACTION100
3.928-4.17390.25441360.21382681X-RAY DIFFRACTION100
4.1739-4.4960.23981640.20542660X-RAY DIFFRACTION100
4.496-4.94810.23381460.20532656X-RAY DIFFRACTION100
4.9481-5.66320.27841360.2342668X-RAY DIFFRACTION100
5.6632-7.13160.30681280.25312725X-RAY DIFFRACTION100
7.1316-49.56250.26761470.25162609X-RAY DIFFRACTION95

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