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- PDB-4z61: The plant peptide hormone receptor complex -

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Basic information

Entry
Database: PDB / ID: 4z61
TitleThe plant peptide hormone receptor complex
Components
  • PTR-ILE-PTR-THR-GLN
  • Phytosulfokine receptor 1
  • Somatic embryogenesis receptor kinase 2
KeywordsTRANSFERASE / hormone receptor / complex
Function / homology
Function and homology information


microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / response to other organism / receptor serine/threonine kinase binding / defense response / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity ...microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / response to other organism / receptor serine/threonine kinase binding / defense response / 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 / signaling receptor binding / protein serine kinase activity / lipid binding / ATP binding / nucleus / plasma membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / 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
Phytosulfokine receptor 1 / Somatic embryogenesis receptor kinase 2
Similarity search - Component
Biological speciesDaucus carota (carrot)
Arabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsChai, J. / Wang, J.
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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Phytosulfokine receptor 1
B: Phytosulfokine receptor 1
C: Somatic embryogenesis receptor kinase 2
D: Somatic embryogenesis receptor kinase 2
P: PTR-ILE-PTR-THR-GLN
Q: PTR-ILE-PTR-THR-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,61823
Polymers190,8576
Non-polymers3,76117
Water3,693205
1
A: Phytosulfokine receptor 1
C: Somatic embryogenesis receptor kinase 2
Q: PTR-ILE-PTR-THR-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,64113
Polymers95,4293
Non-polymers2,21210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phytosulfokine receptor 1
D: Somatic embryogenesis receptor kinase 2
P: PTR-ILE-PTR-THR-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,97710
Polymers95,4293
Non-polymers1,5487
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)486.185, 73.495, 67.333
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-830-

HOH

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Components

#1: Protein Phytosulfokine receptor 1 / DcPSKR1 / Phytosulfokine LRR receptor kinase 1


Mass: 70140.000 Da / Num. of mol.: 2 / Fragment: UNP residues 24-659 / Mutation: A245E, I355L, E368A, A575S, A613D, V625A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daucus carota (carrot) / Gene: PSKR
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q8LPB4, non-specific serine/threonine protein kinase
#2: Protein Somatic embryogenesis receptor kinase 2 / AtSERK2 / Somatic embryogenesis receptor-like kinase 2


Mass: 24441.812 Da / Num. of mol.: 2 / Fragment: UNP residues 1-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK2, At1g34210, F23M19.11
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9XIC7, non-specific serine/threonine protein kinase
#3: Protein/peptide PTR-ILE-PTR-THR-GLN


Mass: 846.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant)
#4: 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.: 17
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate pH 5.5, 0.4M KCl, 30%(v/v) Pentaerythritol propoxylate (5/4 PO/OH)

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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: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→99 Å / Num. obs: 54303 / % possible obs: 88.8 % / Redundancy: 2 % / Net I/σ(I): 14.7

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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 / Resolution: 2.75→29.87 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 2770 5.1 %
Rwork0.196 --
obs0.2 54303 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12227 0 238 205 12670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812715
X-RAY DIFFRACTIONf_angle_d1.43317285
X-RAY DIFFRACTIONf_dihedral_angle_d15.2784674
X-RAY DIFFRACTIONf_chiral_restr0.1132040
X-RAY DIFFRACTIONf_plane_restr0.0082208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.79750.34521160.2381976X-RAY DIFFRACTION68
2.7975-2.84830.37421480.23822613X-RAY DIFFRACTION89
2.8483-2.90310.31851360.22432639X-RAY DIFFRACTION91
2.9031-2.96230.2961290.2322632X-RAY DIFFRACTION90
2.9623-3.02660.31971460.23672617X-RAY DIFFRACTION90
3.0266-3.0970.34241370.23512622X-RAY DIFFRACTION90
3.097-3.17430.31631490.2462617X-RAY DIFFRACTION90
3.1743-3.260.30491370.23572611X-RAY DIFFRACTION90
3.26-3.35580.31751370.22282643X-RAY DIFFRACTION89
3.3558-3.4640.28251570.21762571X-RAY DIFFRACTION89
3.464-3.58760.27621370.19942635X-RAY DIFFRACTION90
3.5876-3.7310.26321380.18442631X-RAY DIFFRACTION89
3.731-3.90050.22841280.16552580X-RAY DIFFRACTION88
3.9005-4.10560.2021210.1562651X-RAY DIFFRACTION89
4.1056-4.36210.19451630.1492607X-RAY DIFFRACTION89
4.3621-4.69770.22911450.1462590X-RAY DIFFRACTION89
4.6977-5.16830.20961320.15082609X-RAY DIFFRACTION88
5.1683-5.91110.2231360.18752598X-RAY DIFFRACTION88
5.9111-7.42840.27261440.21062572X-RAY DIFFRACTION86
7.4284-29.87360.27371340.24332519X-RAY DIFFRACTION82

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