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- PDB-7w5c: Crystal structure of Mitogen Activated Protein Kinase 4 (MPK4) fr... -

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Basic information

Entry
Database: PDB / ID: 7w5c
TitleCrystal structure of Mitogen Activated Protein Kinase 4 (MPK4) from Arabidopsis thaliana
Components
  • Mitogen-activated protein kinase 4
  • Mitogen-activated protein kinase kinase 1
KeywordsTRANSFERASE / MPK4 / Kinase / ATPase / PLANT PROTEIN
Function / homology
Function and homology information


jasmonic acid and ethylene-dependent systemic resistance, jasmonic acid mediated signaling pathway / pollen-pistil interaction / cell plate / male meiosis cytokinesis / jasmonic acid and ethylene-dependent systemic resistance / hypotonic salinity response / cytokinesis by cell plate formation / systemic acquired resistance, salicylic acid mediated signaling pathway / regulation of stomatal closure / defense response to other organism ...jasmonic acid and ethylene-dependent systemic resistance, jasmonic acid mediated signaling pathway / pollen-pistil interaction / cell plate / male meiosis cytokinesis / jasmonic acid and ethylene-dependent systemic resistance / hypotonic salinity response / cytokinesis by cell plate formation / systemic acquired resistance, salicylic acid mediated signaling pathway / regulation of stomatal closure / defense response to other organism / cellular response to carbon dioxide / regulation of stomatal movement / pollen development / response to fungus / mitogen-activated protein kinase kinase / cortical microtubule organization / response to water deprivation / response to abscisic acid / phosphorylation / hyperosmotic response / MAP kinase kinase activity / MAP kinase activity / mitogen-activated protein kinase / response to salt stress / response to cold / response to hydrogen peroxide / response to molecule of bacterial origin / response to wounding / kinase activity / protein tyrosine kinase activity / protein phosphorylation / microtubule / protein kinase activity / defense response to bacterium / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 4 / Mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology
CitationJournal: New Phytol. / Year: 2023
Title: Essential role of the CD docking motif of MPK4 in plant immunity, growth, and development.
Authors: Siodmak, A. / Shahul Hameed, U.F. / Rayapuram, N. / Volz, R. / Boudsocq, M. / Alharbi, S. / Alhoraibi, H. / Lee, Y.H. / Blilou, I. / Arold, S.T. / Hirt, H.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 4
Q: Mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8634
Polymers42,3322
Non-polymers5312
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-22 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.950, 132.950, 132.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Mitogen-activated protein kinase 4 / AtMPK4 / MAP kinase 4


Mass: 40796.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MPK4, At4g01370, F2N1.1, F2N1_2-t
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q39024, mitogen-activated protein kinase
#2: Protein/peptide Mitogen-activated protein kinase kinase 1 / AtMKK1 / MAP kinase kinase 1 / AtMEK1 / NMAPKK


Mass: 1535.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
References: UniProt: Q94A06, mitogen-activated protein kinase kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.201→19.602 Å / Num. obs: 19910 / % possible obs: 99.7 % / Redundancy: 23.6 % / CC1/2: 0.779 / Net I/σ(I): 42.91
Reflection shellResolution: 2.201→2.28 Å / Num. unique obs: 1920 / CC1/2: 0.473

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ERK

2erk


Resolution: 2.201→19.602 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1016 5.11 %
Rwork0.176 --
obs0.1786 19885 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→19.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 32 76 3086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013114
X-RAY DIFFRACTIONf_angle_d1.0914232
X-RAY DIFFRACTIONf_dihedral_angle_d16.181883
X-RAY DIFFRACTIONf_chiral_restr0.062469
X-RAY DIFFRACTIONf_plane_restr0.007547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2012-2.31710.39661360.32912639X-RAY DIFFRACTION99
2.3171-2.4620.32761150.22582703X-RAY DIFFRACTION100
2.462-2.65170.25721760.19672664X-RAY DIFFRACTION100
2.6517-2.91770.24991530.17582658X-RAY DIFFRACTION100
2.9177-3.33810.22631260.17362715X-RAY DIFFRACTION100
3.3381-4.19890.19611490.14662712X-RAY DIFFRACTION100
4.1989-19.6020.19371610.16182778X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 59.0841 Å / Origin y: 38.5997 Å / Origin z: 23.79 Å
111213212223313233
T0.1647 Å20.0172 Å20.0242 Å2-0.2212 Å20.0509 Å2--0.2338 Å2
L0.8981 °20.065 °2-0.5598 °2-0.2766 °2-0.1425 °2--1.0636 °2
S-0.0014 Å °-0.0081 Å °0.0452 Å °-0.0364 Å °-0.065 Å °-0.0261 Å °-0.0337 Å °0.0898 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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