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- PDB-4z64: the plant peptide hormone receptor complex in arabidopsis -

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Basic information

Entry
Database: PDB / ID: 4z64
Titlethe plant peptide hormone receptor complex in arabidopsis
Components
  • Phytosulfokine
  • Phytosulfokine receptor 1
  • Somatic embryogenesis receptor kinase 1
KeywordsHORMONE / hormone receptor complex
Function / homology
Function and homology information


microsporogenesis / floral organ abscission / regulation of defense response / pollen maturation / brassinosteroid mediated signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity ...microsporogenesis / floral organ abscission / regulation of defense response / pollen maturation / brassinosteroid mediated signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / signaling receptor binding / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / ATP binding / identical protein 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, 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-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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Somatic embryogenesis receptor kinase 1 / Phytosulfokine receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.659 Å
AuthorsChai, J. / Wang, J. / Han, Z.
CitationJournal: Nature / Year: 2015
Title: Allosteric receptor activation by the plant peptide hormone phytosulfokine
Authors: Wang, J. / Li, H. / Han, Z. / Zhang, H. / Wang, T. / Lin, G. / Chang, J. / Yang, W. / Chai, J.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_oper_list / pdbx_validate_close_contact / 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 / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_conn.ptnr2_label_seq_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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phytosulfokine receptor 1
C: Somatic embryogenesis receptor kinase 1
P: Phytosulfokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,51217
Polymers94,7123
Non-polymers2,80014
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-27 kcal/mol
Surface area32320 Å2
MethodPISA
2
A: Phytosulfokine receptor 1
P: Phytosulfokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21314
Polymers70,7312
Non-polymers2,48212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-12 kcal/mol
Surface area25690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.539, 220.888, 105.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-309-

MET

21A-309-

MET

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Phytosulfokine receptor 1 / AtPSKR1 / Phytosulfokine LRR receptor kinase 1


Mass: 69884.008 Da / Num. of mol.: 1 / Fragment: UNP resides 24-648
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSKR1, PSKR, At2g02220, F5O4.1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9ZVR7, non-specific serine/threonine protein kinase
#2: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 23981.150 Da / Num. of mol.: 1 / Fragment: UNP residues 1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK1 / Production host: Insect BA phytoplasma (bacteria)
References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Protein/peptide / Non-polymers , 2 types, 5 molecules P

#3: Protein/peptide Phytosulfokine


Mass: 846.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant)
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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Sugars , 2 types, 10 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.: 1
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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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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: 5 Å3/Da / Density % sol: 75.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH4.5, 2.0 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Sep 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→99 Å / Num. obs: 49253 / % possible obs: 96.8 % / Redundancy: 4.2 % / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z5W

4z5w


Resolution: 2.659→48.913 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 2509 5.09 %
Rwork0.2001 --
obs0.2024 49253 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.659→48.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 0 174 0 6364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086517
X-RAY DIFFRACTIONf_angle_d1.2658854
X-RAY DIFFRACTIONf_dihedral_angle_d16.8682411
X-RAY DIFFRACTIONf_chiral_restr0.0841028
X-RAY DIFFRACTIONf_plane_restr0.0051133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6589-2.710.36681220.28642160X-RAY DIFFRACTION81
2.71-2.76530.30821490.27372630X-RAY DIFFRACTION99
2.7653-2.82550.32591340.26552643X-RAY DIFFRACTION99
2.8255-2.89120.33161450.25142661X-RAY DIFFRACTION99
2.8912-2.96350.31911420.2562624X-RAY DIFFRACTION98
2.9635-3.04360.31241540.24682645X-RAY DIFFRACTION98
3.0436-3.13310.29451400.24542636X-RAY DIFFRACTION98
3.1331-3.23430.26351300.23442637X-RAY DIFFRACTION98
3.2343-3.34980.33721280.23142659X-RAY DIFFRACTION98
3.3498-3.48390.27791310.22612650X-RAY DIFFRACTION98
3.4839-3.64240.26631360.20372620X-RAY DIFFRACTION97
3.6424-3.83440.20141600.17642589X-RAY DIFFRACTION97
3.8344-4.07450.2011380.15342620X-RAY DIFFRACTION96
4.0745-4.38890.16871330.14282620X-RAY DIFFRACTION96
4.3889-4.83020.20141450.1532590X-RAY DIFFRACTION95
4.8302-5.52840.20241370.17192617X-RAY DIFFRACTION95
5.5284-6.9620.28161400.22162572X-RAY DIFFRACTION93
6.962-48.92140.23131450.20542571X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: -53.4774 Å / Origin y: -33.4835 Å / Origin z: -8.2839 Å
111213212223313233
T0.646 Å20.077 Å2-0.0413 Å2-0.4757 Å2-0.0458 Å2--0.3152 Å2
L0.716 °2-0.6193 °20.0413 °2-0.9733 °2-0.1559 °2--0.983 °2
S0.0563 Å °-0.0138 Å °-0.0849 Å °0.0714 Å °-0.0148 Å °-0.0809 Å °0.6656 Å °0.1618 Å °-0.0311 Å °
Refinement TLS groupSelection details: all

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