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- PDB-9tyg: Structure of the MAP2K MEK1 in an inactive conformation in comple... -

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Basic information

Entry
Database: PDB / ID: 9tyg
TitleStructure of the MAP2K MEK1 in an inactive conformation in complex with its substrate MAPK ERK2
Components
  • Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
  • Mitogen-activated protein kinase 1
KeywordsSIGNALING PROTEIN / protein kinases / phosphoryl transfer / MAPK / MAP2K / cancer signaling
Function / homology
Function and homology information


symbiont-mediated activation of host MAPK cascade / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / regulation of axon regeneration / mitogen-activated protein kinase kinase ...symbiont-mediated activation of host MAPK cascade / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / regulation of axon regeneration / mitogen-activated protein kinase kinase / Signaling by MAPK mutants / positive regulation of muscle contraction / Golgi inheritance / placenta blood vessel development / MAP-kinase scaffold activity / RAF-independent MAPK1/3 activation / Suppression of apoptosis / cerebellar cortex formation / labyrinthine layer development / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / melanosome transport / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / type B pancreatic cell proliferation / cytosine metabolic process / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / ERKs are inactivated / RSK activation / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / vesicle transport along microtubule / regulation of cellular pH / outer ear morphogenesis / positive regulation of Ras protein signal transduction / Signaling by LTK in cancer / regulation of Golgi inheritance / positive regulation of neuroinflammatory response / central nervous system neuron differentiation / mitogen-activated protein kinase kinase kinase binding / positive regulation of peptidyl-threonine phosphorylation / ERBB signaling pathway / labyrinthine layer blood vessel development / positive regulation of axonogenesis / mammary gland epithelial cell proliferation / chemokine-mediated signaling pathway / trachea formation / triglyceride homeostasis / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / IFNG signaling activates MAPKs / regulation of stress-activated MAPK cascade / Frs2-mediated activation / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / RUNX2 regulates osteoblast differentiation / ciliary tip / ERK/MAPK targets / response to exogenous dsRNA / positive regulation of macrophage chemotaxis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / MAPK1 (ERK2) activation / face development / endodermal cell differentiation / pseudopodium / MAP kinase kinase activity / Bergmann glial cell differentiation / Recycling pathway of L1 / lung morphogenesis / positive regulation of ATP biosynthetic process / positive regulation of telomere maintenance / thyroid gland development / Advanced glycosylation endproduct receptor signaling / Uptake and function of anthrax toxins / positive regulation of protein serine/threonine kinase activity / MAP kinase activity / regulation of ossification / negative regulation of cell differentiation / mitogen-activated protein kinase / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / Signal attenuation / protein kinase activator activity / Growth hormone receptor signaling / phosphatase binding / Schwann cell development / response to axon injury / Estrogen-stimulated signaling through PRKCZ / stress-activated MAPK cascade / keratinocyte differentiation / neuron projection morphogenesis / Nuclear events stimulated by ALK signaling in cancer / ERK1 and ERK2 cascade
Similarity search - Function
: / Mitogen-activated protein (MAP) kinase, ERK1/2 / 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 ...: / Mitogen-activated protein (MAP) kinase, ERK1/2 / 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
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein / Mitogen-activated protein kinase 1 / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Toxoplasma gondii ME49 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
Authorsvon Velsen, J. / Juyoux, P. / Bowler, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2026
Title: Molecular basis of mitogen-activated protein kinase ERK2 activation by its upstream kinase MEK1
Authors: von Velsen, J. / Juyoux, P. / Piasentin, N. / Fisher, H. / Lapouge, K. / Vadas, O. / Gervasio, F.L. / Bowler, M.W.
History
DepositionJan 19, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
B: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5855
Polymers86,7072
Non-polymers8793
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 44981.562 Da / Num. of mol.: 1
Mutation: residue 3-11 replaced with 15 residues GRA24 KIM,Ser218Asp,Ser222Asp
Source method: isolated from a genetically manipulated source
Details: protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.,protein chimera ...Details: protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.,protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.,protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.,protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.,protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.,protein chimera of human MEK1, exchanging native KIM (r3-11) by GRA24 KIM (15 residues). Addition of activating mutations on serines in activation-loop: Ser218Asp, Ser222Asp.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Toxoplasma gondii ME49 (eukaryote)
Gene: MAP2K1, MEK1, PRKMK1, TGME49_230180 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q02750, UniProt: A0A125YG37, mitogen-activated protein kinase kinase
#2: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 41724.977 Da / Num. of mol.: 1 / Mutation: Thr185Val
Source method: isolated from a genetically manipulated source
Details: ERK2 with point mutation on residue 185 to a valine
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P28482, mitogen-activated protein kinase
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*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
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Complex between the MAP2K MEK1 and its substrate MAPK ERK2COMPLEX#1-#20RECOMBINANT
2MEK1DDGRAORGANELLE OR CELLULAR COMPONENT#11RECOMBINANThuman MEK1 with KIM motif exchanged to GRA24 KIM (15 residues).
3ERK2ORGANELLE OR CELLULAR COMPONENT#21RECOMBINANThuman ERK2 with point mutation on T185V.
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
1186.6 kDa/nmNO
2144.9 kDa/nmNO
3141.7 kDa/nmNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Trichoplusia ni (cabbage looper)7111HighFive
32Trichoplusia ni (cabbage looper)7111HighFive
43Escherichia coli (E. coli)562Rosetta2
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES pH 7.51
2200 mMsodium chlorideNaCl1
310 mMmagnesium chlorideMgCl21
45 %Glycerol1
50.5 mMTCEP1
SpecimenConc.: 0.516 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 250 uM ADP.AlF4- was added to the sample
Specimen supportGrid material: GOLD / Grid type: HexAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 270000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.7 sec. / Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 88517
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv4.7.0particle selectionblob picker then Topaz
2PHENIX1.21.2_5419+SVNmodel refinement
5cryoSPARCv4.7.0CTF correctionPatch CTF
13cryoSPARCv4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142124 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 156.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00265355
ELECTRON MICROSCOPYf_angle_d0.65657252
ELECTRON MICROSCOPYf_chiral_restr0.0453796
ELECTRON MICROSCOPYf_plane_restr0.0036924
ELECTRON MICROSCOPYf_dihedral_angle_d5.0941725

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