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- EMDB-56418: Structure of the MAP2K MEK1 in an inactive conformation in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-56418
TitleStructure of the MAP2K MEK1 in an inactive conformation in complex with its substrate MAPK ERK2
Map datarefined map of MEK1DDGRA-ERK2T185V
Sample
  • Complex: Complex between the MAP2K MEK1 and its substrate MAPK ERK2
    • Organelle or cellular component: MEK1DDGRA
      • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
    • Organelle or cellular component: ERK2
      • Protein or peptide: Mitogen-activated protein kinase 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsprotein kinases / phosphoryl transfer / MAPK / MAP2K / cancer signaling / SIGNALING PROTEIN
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
Uncharacterized protein / Mitogen-activated protein kinase 1 / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
Authorsvon Velsen J / Juyoux P / Bowler MW
Funding support1 items
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 FL / Bowler MW
History
DepositionJan 19, 2026-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56418.png

Downloads & links

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Map

FileDownload / File: emd_56418.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined map of MEK1DDGRA-ERK2T185V
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 220 pix.
= 202.4 Å		0.92 Å/pix.
x 220 pix.
= 202.4 Å		0.92 Å/pix.
x 220 pix.
= 202.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0669
Minimum - Maximum-0.20678288 - 0.5856031
Average (Standard dev.)0.0006000431 (±0.0128877675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 202.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56418_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map of MEK1DDGRA-T185V

Fileemd_56418_additional_1.map
AnnotationB-factor sharpened map of MEK1DDGRA-T185V
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_56418_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_56418_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Complex between the MAP2K MEK1 and its substrate MAPK ERK2

EntireName: Complex between the MAP2K MEK1 and its substrate MAPK ERK2
Components
  • Complex: Complex between the MAP2K MEK1 and its substrate MAPK ERK2
    • Organelle or cellular component: MEK1DDGRA
      • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
    • Organelle or cellular component: ERK2
      • Protein or peptide: Mitogen-activated protein kinase 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex between the MAP2K MEK1 and its substrate MAPK ERK2

SupramoleculeName: Complex between the MAP2K MEK1 and its substrate MAPK ERK2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.7 kDa/nm

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Supramolecule #2: MEK1DDGRA

SupramoleculeName: MEK1DDGRA / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: human MEK1 with KIM motif exchanged to GRA24 KIM (15 residues).
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: ERK2

SupramoleculeName: ERK2 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: human ERK2 with point mutation on T185V.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dual specificity mitogen-activated protein kinase kinase 1,Unchar...

MacromoleculeName: Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
type: protein_or_peptide / ID: 1
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.
Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.981562 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPLLERRGVS ELPPLYINPA PDGSAVNGTS SAETNLEALQ KKLEELELDE QQRKRLEAFL TQKQKVGELK DDDFEKISEL GAGNGGVVF KVSHKPSGLV MARKLIHLEI KPAIRNQIIR ELQVLHECNS PYIVGFYGAF YSDGEISICM EHMDGGSLDQ V LKKAGRIP ...String:
MPLLERRGVS ELPPLYINPA PDGSAVNGTS SAETNLEALQ KKLEELELDE QQRKRLEAFL TQKQKVGELK DDDFEKISEL GAGNGGVVF KVSHKPSGLV MARKLIHLEI KPAIRNQIIR ELQVLHECNS PYIVGFYGAF YSDGEISICM EHMDGGSLDQ V LKKAGRIP EQILGKVSIA VIKGLTYLRE KHKIMHRDVK PSNILVNSRG EIKLCDFGVS GQLIDDMAND FVGTRSYMSP ER LQGTHYS VQSDIWSMGL SLVEMAVGRY PIPPPDAKEL ELMFGCQVEG DAAETPPRPR TPGRPLSSYG MDSRPPMAIF ELL DYIVNE PPPKLPSGVF SLEFQDFVNK CLIKNPAERA DLKQLMVHAF IKRSDAEEVD FAGWLCSTIG LNQPSTPTHA AGVL EVLFQ

UniProtKB: Dual specificity mitogen-activated protein kinase kinase 1, Uncharacterized protein, Dual specificity mitogen-activated protein kinase kinase 1

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Macromolecule #2: Mitogen-activated protein kinase 1

MacromoleculeName: Mitogen-activated protein kinase 1 / type: protein_or_peptide / ID: 2
Details: ERK2 with point mutation on residue 185 to a valine
Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.724977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QGPMAAAAAA GAGPEMVRGQ VFDVGPRYTN LSYIGEGAYG MVCSAYDNVN KVRVAIKKIS PFEHQTYCQR TLREIKILLR FRHENIIGI NDIIRAPTIE QMKDVYIVQD LMETDLYKLL KTQHLSNDHI CYFLYQILRG LKYIHSANVL HRDLKPSNLL L NTTCDLKI ...String:
QGPMAAAAAA GAGPEMVRGQ VFDVGPRYTN LSYIGEGAYG MVCSAYDNVN KVRVAIKKIS PFEHQTYCQR TLREIKILLR FRHENIIGI NDIIRAPTIE QMKDVYIVQD LMETDLYKLL KTQHLSNDHI CYFLYQILRG LKYIHSANVL HRDLKPSNLL L NTTCDLKI CDFGLARVAD PDHDHTGFLV EYVATRWYRA PEIMLNSKGY TKSIDIWSVG CILAEMLSNR PIFPGKHYLD QL NHILGIL GSPSQEDLNC IINLKARNYL LSLPHKNKVP WNRLFPNADS KALDLLDKML TFNPHKRIEV EQALAHPYLE QYY DPSDEP IAEAPFKFDM ELDDLPKEKL KELIFEETAR FQPGYRS

UniProtKB: Mitogen-activated protein kinase 1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.516 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES pH 7.5
200.0 mMsodium chlorideNaCl
10.0 mMmagnesium chlorideMgCl2
5.0 %Glycerol
0.5 mMTCEP
GridModel: HexAuFoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV
Details250 uM ADP.AlF4- was added to the sample

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 88517 / Average exposure time: 1.7 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 270000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.0) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.0) / Number images used: 142124
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9tyg:
Structure of the MAP2K MEK1 in an inactive conformation in complex with its substrate MAPK ERK2

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