[English] 日本語
Yorodumi
- PDB-7w5c: Crystal structure of Mitogen Activated Protein Kinase 4 (MPK4) fr... -

+
Open data


ID or keywords:

Loading...

-
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 / cytokinesis by cell plate formation / hypotonic salinity response / cellular response to carbon dioxide / systemic acquired resistance, salicylic acid mediated signaling pathway / 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 / cytokinesis by cell plate formation / hypotonic salinity response / cellular response to carbon dioxide / systemic acquired resistance, salicylic acid mediated signaling pathway / defense response to other organism / regulation of stomatal closure / response to fungus / pollen development / regulation of stomatal movement / response to abscisic acid / cortical microtubule organization / response to water deprivation / mitogen-activated protein kinase kinase / hyperosmotic response / MAP kinase kinase activity / MAP kinase activity / mitogen-activated protein kinase / phosphorylation / response to salt stress / response to cold / response to molecule of bacterial origin / response to hydrogen peroxide / response to wounding / kinase activity / protein tyrosine kinase activity / microtubule / protein kinase activity / defense response to bacterium / protein phosphorylation / 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. / : / 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. ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more