[English] 日本語
Yorodumi
- EMDB-56419: Structure of the MAP2K MEK1 in an active conformation in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-56419
TitleStructure of the MAP2K MEK1 in an active 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: Mitogen-activated protein kinase 1
    • Organelle or cellular component: ERK2
      • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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) / Toxoplasma gondii ME49 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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

-
Structure visualization

Supplemental images

emd_56419.png

Downloads & links

-
Map

FileDownload / File: emd_56419.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: 0.0933
Minimum - Maximum-0.24222286 - 0.5304156
Average (Standard dev.)0.00039664545 (±0.014388874)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_56419_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: B-factor sharpened map.

Fileemd_56419_additional_1.map
AnnotationB-factor sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_56419_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_56419_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: Mitogen-activated protein kinase 1
    • Organelle or cellular component: ERK2
      • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1,Uncharacterized protein,Dual specificity mitogen-activated protein kinase kinase 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
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

-
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)

-
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)

-
Macromolecule #1: Mitogen-activated protein kinase 1

MacromoleculeName: Mitogen-activated protein kinase 1 / type: protein_or_peptide / ID: 1
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

-
Macromolecule #2: 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: 2
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: Toxoplasma gondii ME49 (eukaryote)
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.0) / Number images used: 113564
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
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-9tyh:
Structure of the MAP2K MEK1 in an active conformation in complex with its substrate MAPK ERK2

+
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