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- PDB-5iyv: Crystal structure of the Arabidopsis receptor kinase HAESA LRR ec... -

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Basic information

Entry
Database: PDB / ID: 5iyv
TitleCrystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain in complex with the peptide hormone IDL1.
Components
  • Protein IDA-LIKE 1
  • Receptor-like protein kinase 5
KeywordsSIGNALING PROTEIN / membrane receptor kinase / peptide hormone receptor / signaling complex / plant development / organ shedding
Function / homology
Function and homology information


lateral root morphogenesis / leaf abscission / floral organ abscission / pectin catabolic process / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / regulation of gene expression / defense response to Gram-negative bacterium / protein autophosphorylation / non-specific serine/threonine protein kinase ...lateral root morphogenesis / leaf abscission / floral organ abscission / pectin catabolic process / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / regulation of gene expression / defense response to Gram-negative bacterium / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / extracellular space / ATP 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 / 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 ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / 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
Receptor-like protein kinase 5 / Protein IDA-LIKE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.56 Å
AuthorsSantiago, J. / Hothorn, M.
CitationJournal: Elife / Year: 2016
Title: Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission.
Authors: Santiago, J. / Brandt, B. / Wildhagen, M. / Hohmann, U. / Hothorn, L.A. / Butenko, M.A. / Hothorn, M.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-like protein kinase 5
B: Protein IDA-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,27310
Polymers68,5262
Non-polymers2,7488
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint30 kcal/mol
Surface area26070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.181, 150.181, 60.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Receptor-like protein kinase 5 / Protein HAESA


Mass: 67216.195 Da / Num. of mol.: 1 / Fragment: ectodomain, residues 20-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: abscission zone / Gene: RLK5, HAE, At4g28490, F21O9.180 / Organ: flowers / Cell line (production host): BTI38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P47735, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide Protein IDA-LIKE 1


Mass: 1309.495 Da / Num. of mol.: 1 / Fragment: UNP residues 67-78 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q29PV4

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Sugars , 3 types, 7 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: 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
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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.: 3
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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Non-polymers , 2 types, 10 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 22% PEG 3350, 0.2 M MgCl2, 0.1 M citric acid pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 25124 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 15 % / CC1/2: 1 / Rsym value: 0.054 / Net I/σ(I): 25.97
Reflection shellResolution: 2.56→2.72 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 1.91 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0135refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5IXO

5ixo


Resolution: 2.56→49.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 29.911 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.502 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23107 1288 5.1 %RANDOM
Rwork0.19091 ---
obs0.19294 23835 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 89.4 Å2
Baniso -1Baniso -2Baniso -3
1--4 Å2-2 Å2-0 Å2
2---4 Å20 Å2
3---12.99 Å2
Refinement stepCycle: 1 / Resolution: 2.56→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 180 9 4744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194880
X-RAY DIFFRACTIONr_bond_other_d0.0010.024657
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0396666
X-RAY DIFFRACTIONr_angle_other_deg1.047310799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.18925.989187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60315804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.621515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215425
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02996
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2166.4932413
X-RAY DIFFRACTIONr_mcbond_other2.2166.4922412
X-RAY DIFFRACTIONr_mcangle_it3.3689.743015
X-RAY DIFFRACTIONr_mcangle_other3.3679.7413016
X-RAY DIFFRACTIONr_scbond_it3.3177.2532465
X-RAY DIFFRACTIONr_scbond_other3.3157.2542465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.20910.773642
X-RAY DIFFRACTIONr_long_range_B_refined8.16463.74519683
X-RAY DIFFRACTIONr_long_range_B_other8.16463.74619684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.564→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 107 -
Rwork0.396 1685 -
obs--97.23 %
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)
16.7425-0.07211.06385.70931.57215.8724-0.2234-0.1680.835-0.0490.31110.7453-0.806-0.2356-0.08770.18510.12850.01490.14490.03310.2425-12.747686.4811-15.5683
22.1665-2.35780.89393.7723-0.84971.24570.19440.36810.0453-0.265-0.251-0.304-0.05820.10550.05660.05280.0198-0.01870.10880.00910.11737.506669.0545-13.6705
33.11020.3569-1.56922.4244-0.7844.91770.0419-0.598-0.21690.367-0.1126-0.4765-0.01160.20860.07060.1510.0161-0.15690.15910.09140.333717.137352.088411.9488
44.52932.59240.36211.92280.43111.58850.3495-1.10970.00540.6489-0.5427-0.04640.2694-0.48490.19320.5467-0.0941-0.08570.72120.15950.2895-1.522143.791926.2935
54.51562.32232.18074.75570.57152.24930.4777-0.9177-0.50660.5438-0.6090.09190.2769-0.32110.13120.4799-0.27390.17390.7950.24440.3933-22.828424.486320.8507
63.6687-3.7508-1.14543.85131.16390.36240.14010.288-0.3445-0.082-0.22960.3389-0.0681-0.12190.08950.42890.0033-0.11790.5860.00850.39142.944758.5023-0.4199
70.202-0.23530.6091.0557-3.860714.56960.0364-0.2664-0.10380.11980.08750.101-0.55060.061-0.12390.3658-0.0560.02650.48630.07750.58951.940747.14339.6086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 56
2X-RAY DIFFRACTION2A57 - 244
3X-RAY DIFFRACTION3A245 - 355
4X-RAY DIFFRACTION4A356 - 461
5X-RAY DIFFRACTION5A462 - 608
6X-RAY DIFFRACTION6B67 - 73
7X-RAY DIFFRACTION7B74 - 78

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