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

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Basic information

Entry
Database: PDB / ID: 5ixo
TitleCrystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain (apo form).
ComponentsReceptor-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 / floral organ abscission / leaf abscission / pectin catabolic process / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity ...lateral root morphogenesis / floral organ abscission / leaf abscission / pectin catabolic process / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / regulation of gene expression / protein autophosphorylation / defense response to Gram-negative bacterium / 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 / protein serine kinase activity / 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 ...: / 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
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.74 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 23, 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_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 / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id
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: Receptor-like protein kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,30110
Polymers67,2161
Non-polymers2,0859
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint19 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.678, 148.678, 58.041
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 , 1 types, 1 molecules A

#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: flower / Plasmid: pBAC3mod / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI38
References: UniProt: P47735, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 2 types, 6 molecules

#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: 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 , 3 types, 81 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 22% PEG 3350, 0.2 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: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.74→128.76 Å / Num. obs: 74928 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 81.1 Å2 / CC1/2: 1 / Rsym value: 0.048 / Net I/σ(I): 18.7
Reflection shellResolution: 1.74→1.85 Å / Redundancy: 14 % / Mean I/σ(I) obs: 1.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.74→128.76 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 7.857 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22172 3713 5 %RANDOM
Rwork0.1802 ---
obs0.18227 71213 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.252 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20.74 Å20 Å2
2--1.47 Å2-0 Å2
3----4.78 Å2
Refinement stepCycle: 1 / Resolution: 1.74→128.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 135 78 4721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194762
X-RAY DIFFRACTIONr_bond_other_d0.0020.024536
X-RAY DIFFRACTIONr_angle_refined_deg2.2592.0226488
X-RAY DIFFRACTIONr_angle_other_deg1.173310497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.56326.022186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99915790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4511514
X-RAY DIFFRACTIONr_chiral_restr0.1470.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215354
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02990
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_it3.7065.6232391
X-RAY DIFFRACTIONr_mcbond_other3.6965.6232390
X-RAY DIFFRACTIONr_mcangle_it4.2278.4082989
X-RAY DIFFRACTIONr_mcangle_other4.238.4082990
X-RAY DIFFRACTIONr_scbond_it5.766.2952368
X-RAY DIFFRACTIONr_scbond_other5.766.2952368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6099.2443495
X-RAY DIFFRACTIONr_long_range_B_refined8.35555.13720122
X-RAY DIFFRACTIONr_long_range_B_other8.35655.13220116
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.743→1.788 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.543 321 -
Rwork0.514 4952 -
obs--95.15 %
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)
15.9250.2556-0.28552.8558-0.05916.1967-0.0588-0.3730.5647-0.0552-0.09640.4678-0.6708-0.27460.15520.10550.0725-0.07350.12690.0130.4669-13.65884.812-14.999
21.2349-0.97930.43632.3734-0.69820.8730.04020.11570.11-0.1947-0.0786-0.01590.01390.02560.03840.02070.00290.01140.01130.00540.36288.73365.946-11.129
31.69110.6734-0.08892.10790.13032.28540.1595-0.28460.05610.2162-0.1990.03980.0023-0.0930.03950.029-0.03480.01710.0572-0.01230.35179.72147.70220.57
43.68452.80250.84393.70350.16491.16060.4631-0.6920.12560.1636-0.51620.31140.1159-0.30050.05310.1269-0.15320.04760.3339-0.02580.3759-20.31426.68921.611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 55
2X-RAY DIFFRACTION2A56 - 275
3X-RAY DIFFRACTION3A276 - 423
4X-RAY DIFFRACTION4A424 - 615

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