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- PDB-5ixt: The crystal structure of the Arabidopsis receptor kinase HAESA LR... -

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Basic information

Entry
Database: PDB / ID: 5ixt
TitleThe crystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain in complex with a N-terminal extended IDA peptide hormone ligand.
Components
  • Protein IDA
  • 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 / regulation of cell diameter / floral organ abscission / leaf abscission / response to ethylene / pectin catabolic process / apoplast / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation ...lateral root morphogenesis / regulation of cell diameter / floral organ abscission / leaf abscission / response to ethylene / pectin catabolic process / apoplast / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / regulation of gene expression / defense response to Gram-negative bacterium / non-specific serine/threonine protein kinase / protein kinase activity / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...Protein IDA-like / : / 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
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,87812
Polymers69,0812
Non-polymers2,79610
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint16 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.921, 148.921, 58.022
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: 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
#2: Protein/peptide Protein IDA / Protein INFLORESCENCE DEFICIENT IN ABSCISSION


Mass: 1865.140 Da / Num. of mol.: 1 / Fragment: UNP residues 53-69 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LAD7

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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 , 3 types, 43 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 23% PEG 3350,0.2M MgCl2,0.1M citric acid pH4

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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: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.94→128.97 Å / Num. obs: 54201 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 81.7 Å2 / CC1/2: 1 / Rsym value: 0.035 / Net I/σ(I): 20.9
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.4 / % possible all: 97.9

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Processing

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

5ixo


Resolution: 1.94→128.97 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 8.142 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20763 2644 4.9 %RANDOM
Rwork0.17926 ---
obs0.18068 51557 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å2-0 Å2
3----3.82 Å2
Refinement stepCycle: 1 / Resolution: 1.94→128.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 182 40 4829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194931
X-RAY DIFFRACTIONr_bond_other_d0.0020.024698
X-RAY DIFFRACTIONr_angle_refined_deg1.82.0366733
X-RAY DIFFRACTIONr_angle_other_deg1.124310894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725.032620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.98426190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65415808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.051515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215483
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021008
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_it2.6946.0292439
X-RAY DIFFRACTIONr_mcbond_other2.6956.0282438
X-RAY DIFFRACTIONr_mcangle_it3.1959.023047
X-RAY DIFFRACTIONr_mcangle_other3.1949.023048
X-RAY DIFFRACTIONr_scbond_it4.0766.7762490
X-RAY DIFFRACTIONr_scbond_other4.0756.7762490
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8789.9963678
X-RAY DIFFRACTIONr_long_range_B_refined6.69848.8245157
X-RAY DIFFRACTIONr_long_range_B_other6.69848.8245157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.944→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 195 -
Rwork0.356 3640 -
obs--95.97 %
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)
13.36080.3951-0.6774.8068-0.08026.5375-0.0726-0.13240.2730.00750.06520.2443-0.5651-0.19010.00740.06340.0363-0.0420.0545-0.00180.2738-12.776185.7049-15.0204
21.0117-0.79180.33051.8574-0.25030.78450.04370.15840.073-0.1767-0.0763-0.04330.02180.05770.03270.01840.00150.00310.02680.01670.23367.313468.1126-13.5796
30.78740.2644-0.57061.5821-0.10662.90450.0406-0.14790.00370.1422-0.1064-0.15840.01630.21040.06580.0320.0049-0.01780.0480.00280.273416.919951.422112.0762
42.83831.2560.18762.22890.09681.36190.1733-0.3750.0710.3752-0.21610.16520.0981-0.1930.04280.1576-0.07010.030.1315-0.01310.2384-1.838543.189326.3739
52.77491.27861.24032.570.09862.86190.3013-0.2629-0.02550.2623-0.25190.24950.3316-0.3528-0.04940.2385-0.12490.06020.24690.00710.2784-22.93323.385820.1218
66.26835.13264.682712.47925.51464.2272-0.41140.07710.4528-0.5467-0.08140.7944-0.3063-0.4270.49290.0964-0.03920.05840.5478-0.02070.38292.120857.364-0.2241
73.24284.0596-2.5499.0265-5.33933.7946-0.21790.1578-0.1452-0.34910.187-0.01150.2285-0.38930.03090.17470.00150.00670.1702-0.01230.20551.785147.04298.5856
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 - 615
6X-RAY DIFFRACTION6B58 - 64
7X-RAY DIFFRACTION7B65 - 69

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