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- PDB-5iyx: Crystal structure of the Arabidopsis receptor kinase HAESA in com... -

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Basic information

Entry
Database: PDB / ID: 5iyx
TitleCrystal structure of the Arabidopsis receptor kinase HAESA in complex with the peptide hormone IDA and the co-receptor SERK1
Components
  • Protein IDA
  • Receptor-like protein kinase 5
  • Somatic embryogenesis receptor kinase 1
KeywordsSIGNALING PROTEIN / membrane receptor kinase / peptide hormone receptor / signaling complex / plant development / organ shedding
Function / homology
Function and homology information


lateral root morphogenesis / regulation of cell diameter / microsporogenesis / leaf abscission / floral organ abscission / pollen maturation / response to ethylene / brassinosteroid mediated signaling pathway / pectin catabolic process / embryo development ending in seed dormancy ...lateral root morphogenesis / regulation of cell diameter / microsporogenesis / leaf abscission / floral organ abscission / pollen maturation / response to ethylene / brassinosteroid mediated signaling pathway / pectin catabolic process / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / apoplast / receptor serine/threonine kinase binding / Golgi organization / 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 phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Protein IDA-like / 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 / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Protein IDA-like / 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 / Alpha-Beta Horseshoe / 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 / 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
Receptor-like protein kinase 5 / Protein IDA / Somatic embryogenesis receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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_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.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 / 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: Receptor-like protein kinase 5
B: Protein IDA
C: Somatic embryogenesis receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,71613
Polymers95,0093
Non-polymers2,70710
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint38 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.507, 100.456, 142.759
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 AC

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


Mass: 71675.945 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: abcsission / Gene: RLK5, HAE, At4g28490, F21O9.180 / Organ: flower / Plasmid: pBAC3mod / Cell line (production host): BTI38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P47735, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#3: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 21751.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N115D and N163Q / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: abscission zone / Gene: SERK1, At1g71830, F14O23.21, F14O23_24 / Organ: flower / Plasmid: pBAC3mod / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI38
References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Protein/peptide , 1 types, 1 molecules B

#2: Protein/peptide Protein IDA / Protein INFLORESCENCE DEFICIENT IN ABSCISSION


Mass: 1581.793 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 56-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: abscission zone / Gene: IDA, At1g68765, F14K14 / Organ: flower / Plasmid: pBAC3mod / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI38 / References: UniProt: Q8LAD7

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Sugars , 2 types, 8 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.: 4
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.: 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

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Non-polymers , 2 types, 137 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% PEG 8,000, 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: 1.00002 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 41023 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 59.3 Å2 / CC1/2: 0.999 / Rsym value: 0.107 / Net I/σ(I): 16.1
Reflection shellResolution: 2.43→2.57 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.96 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IXO, 4LSC

5ixo

4lsc


Resolution: 2.43→47.38 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 20.027 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23435 2051 5 %RANDOM
Rwork0.19266 ---
obs0.19478 38969 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.535 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å2-0 Å2-0 Å2
2---2.1 Å20 Å2
3---4.84 Å2
Refinement stepCycle: LAST / Resolution: 2.43→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 176 135 6377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196389
X-RAY DIFFRACTIONr_bond_other_d0.0020.026099
X-RAY DIFFRACTIONr_angle_refined_deg1.412.0228718
X-RAY DIFFRACTIONr_angle_other_deg1.038314104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.69525.882255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.116151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081522
X-RAY DIFFRACTIONr_chiral_restr0.0760.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217162
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021332
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_it0.9183.5543185
X-RAY DIFFRACTIONr_mcbond_other0.9173.5543184
X-RAY DIFFRACTIONr_mcangle_it1.5145.333977
X-RAY DIFFRACTIONr_mcangle_other1.5145.333978
X-RAY DIFFRACTIONr_scbond_it1.5573.9063204
X-RAY DIFFRACTIONr_scbond_other1.5563.9073205
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5645.7954740
X-RAY DIFFRACTIONr_long_range_B_refined6.02434.927302
X-RAY DIFFRACTIONr_long_range_B_other6.02534.89827298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.427→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 138 -
Rwork0.41 2631 -
obs--92.09 %
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)
10.9468-1.3398-0.88327.47930.33714.91750.2727-0.57320.25261.0344-0.1948-0.2353-0.465-0.4167-0.07790.5697-0.2930.21940.9539-0.10870.32325.11682.968117.8478
24.56740.81780.87251.92460.48245.59060.0714-0.78260.50710.58830.03990.1402-0.55820.0156-0.11140.3607-0.0250.08230.4893-0.04380.130712.78387.13768.6142
32.4141-0.2124-0.53092.76021.04262.85760.173-0.25230.3690.16490.0215-0.3425-0.55020.2819-0.19450.1795-0.0740.00510.2797-0.01690.093626.95348.0868-11.5663
42.665-0.26790.40784.2457-0.07973.14290.08120.04310.02810.08160.0095-0.7342-0.12270.5861-0.09070.0134-0.0352-0.01440.3037-0.02480.13840.2763-11.2472-21.5957
52.95431.48611.12423.20650.44661.27730.2078-0.0331-0.68550.1138-0.0262-0.31420.41340.1115-0.18160.15330.0839-0.02070.2593-0.01040.170826.8479-36.5669-25.0747
63.25010.67441.68151.87251.59143.79110.26730.078-0.4925-0.07090.0213-0.02790.6085-0.367-0.28870.2325-0.0578-0.0810.2082-0.00520.1470.1699-45.9696-40.2739
71.6377-3.4215-0.78417.96473.7325.8629-0.14540.0536-0.3180.106-0.13050.7264-0.3717-0.23530.27580.0842-0.0720.00010.24650.03630.07620.8615-10.2218-14.8246
82.51040.4931-1.79158.6416-1.51899.86660.2903-0.08560.5196-0.0257-0.1018-0.1942-0.73740.1423-0.18850.1329-0.032-0.01170.2024-0.03820.19739.5884-15.852-25.1108
912.40372.6396-1.43222.6915-0.15050.1780.3001-0.3434-0.19710.4927-0.31170.09-0.00250.01340.01150.1122-0.0273-0.01280.2574-0.01850.080310.9235-23.065-20.3612
105.10352.88910.17556.6776-1.97859.9285-0.1590.3087-0.5541-0.1079-0.0762-0.40880.31220.25720.23520.01820.01050.0250.1135-0.02520.067112.2604-26.0975-31.7889
115.30450.98350.36231.64240.34532.956-0.08290.04680.66060.0076-0.00110.2461-0.3233-0.09530.08390.03790.0041-0.00970.1512-0.00440.0934-4.5181-21.8675-34.4
125.81331.3641-2.05254.1224-0.27497.18120.02440.51560.1795-0.5240.18850.26930.3805-0.5815-0.21290.1011-0.0371-0.04230.3093-0.04140.0937-17.505-26.209-40.9522
138.6444-0.8075-3.39240.19860.05664.7740.36080.1987-0.1888-0.24420.0410.27230.2568-1.2047-0.40180.4031-0.1131-0.39910.47310.06170.6024-25.3148-25.258-39.2838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 55
2X-RAY DIFFRACTION2A56 - 124
3X-RAY DIFFRACTION3A125 - 270
4X-RAY DIFFRACTION4A271 - 337
5X-RAY DIFFRACTION5A338 - 520
6X-RAY DIFFRACTION6A521 - 616
7X-RAY DIFFRACTION7B56 - 69
8X-RAY DIFFRACTION8C26 - 39
9X-RAY DIFFRACTION9C40 - 59
10X-RAY DIFFRACTION10C60 - 75
11X-RAY DIFFRACTION11C76 - 171
12X-RAY DIFFRACTION12C172 - 194
13X-RAY DIFFRACTION13C195 - 211

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