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- EMDB-64516: The complex of human pMEK1 and uERK1 (ANP) -

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Basic information

Entry
Database: EMDB / ID: EMD-64516
TitleThe complex of human pMEK1 and uERK1 (ANP)
Map data
Sample
  • Complex: The complex of human pMEK1 and uERK1 at the presence of AMPPNP
    • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
    • Protein or peptide: Mitogen-activated protein kinase 3
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsMEK1. ERK1 / Complex / Kinase / MAPK pathway / TRANSFERASE
Function / homology
Function and homology information


negative regulation of cholesterol efflux / negative regulation of homotypic cell-cell adhesion / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of xenophagy / xenophagy / regulation of vascular associated smooth muscle contraction / mitogen-activated protein kinase kinase / negative regulation of T cell mediated immune response to tumor cell ...negative regulation of cholesterol efflux / negative regulation of homotypic cell-cell adhesion / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of xenophagy / xenophagy / regulation of vascular associated smooth muscle contraction / mitogen-activated protein kinase kinase / negative regulation of T cell mediated immune response to tumor cell / positive regulation of muscle contraction / Golgi inheritance / placenta blood vessel development / MAP kinase scaffold activity / RAF-independent MAPK1/3 activation / Suppression of apoptosis / regulation of axon regeneration / 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 / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / peptidyl-tyrosine autophosphorylation / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / RSK activation / ERKs are inactivated / positive regulation of cyclase activity / phosphorylation / type B pancreatic cell proliferation / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / central nervous system neuron differentiation / cartilage development / outer ear morphogenesis / vesicle transport along microtubule / positive regulation of Ras protein signal transduction / : / Signaling by LTK in cancer / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / interleukin-1-mediated signaling pathway / positive regulation of axonogenesis / 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 / positive regulation of neuroinflammatory response / Frs2-mediated activation / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / Activation of the AP-1 family of transcription factors / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / ERK/MAPK targets / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / face development / endodermal cell differentiation / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / MAP kinase kinase activity / Bergmann glial cell differentiation / positive regulation of protein serine/threonine kinase activity / lung morphogenesis / thyroid gland development / pseudopodium / positive regulation of telomere maintenance / positive regulation of ATP biosynthetic process / Advanced glycosylation endproduct receptor signaling / Uptake and function of anthrax toxins / MAP kinase activity / regulation of ossification / 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 / protein kinase activator activity / Signal attenuation / BMP signaling pathway / Growth hormone receptor signaling / Schwann cell development / response to axon injury / stress-activated MAPK cascade / phosphatase binding / keratinocyte differentiation / neuron projection morphogenesis / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / phosphotyrosine residue binding / myelination
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
Mitogen-activated protein kinase 3 / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsPeng C / Sun Y / Liu S / Zhou F / Hu Q
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2023C03109 China
CitationJournal: Biorxiv / Year: 2026
Title: Mechanistic insight into the phosphorylation of ERK by MEK
Authors: Sun Y / Peng C / Liu S / Zhou F / Huang G / Wang J / Hu Q
History
DepositionMay 8, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64516.png

Downloads & links

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Map

FileDownload / File: emd_64516.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 206.842 Å		1.08 Å/pix.
x 192 pix.
= 206.842 Å		1.08 Å/pix.
x 192 pix.
= 206.842 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66
Minimum - Maximum-4.7871766 - 6.474084
Average (Standard dev.)0.000550464 (±0.17306413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 206.84158 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64516_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64516_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of human pMEK1 and uERK1 at the presence of AMPPNP

EntireName: The complex of human pMEK1 and uERK1 at the presence of AMPPNP
Components
  • Complex: The complex of human pMEK1 and uERK1 at the presence of AMPPNP
    • Protein or peptide: Dual specificity mitogen-activated protein kinase kinase 1
    • Protein or peptide: Mitogen-activated protein kinase 3
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The complex of human pMEK1 and uERK1 at the presence of AMPPNP

SupramoleculeName: The complex of human pMEK1 and uERK1 at the presence of AMPPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dual specificity mitogen-activated protein kinase kinase 1

MacromoleculeName: Dual specificity mitogen-activated protein kinase kinase 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.00132 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKKKPTPIQ LNPAPDGSAV NGTSSAETNL EALQKKLEEL ELDEQQRKRL EAFLTQKQKV GELKDDDFEK ISELGAGNGG VVFKVSHKP SGLVMARKLI HLEIKPAIRN QIIRELQVLH ECNSPYIVGF YGAFYSDGEI SICMEHMDGG SLDQVLKKAG R IPEQILGK ...String:
MPKKKPTPIQ LNPAPDGSAV NGTSSAETNL EALQKKLEEL ELDEQQRKRL EAFLTQKQKV GELKDDDFEK ISELGAGNGG VVFKVSHKP SGLVMARKLI HLEIKPAIRN QIIRELQVLH ECNSPYIVGF YGAFYSDGEI SICMEHMDGG SLDQVLKKAG R IPEQILGK VSIAVIKGLT YLREKHKIMH RDVKPSNILV NSRGEIKLCD FGVSGQLID(SEP) MAN(SEP)FVGTRS YMSP ERLQG THYSVQSDIW SMGLSLVEMA VGRYPIPPPD AKELELMFGC QVEGDAAETP PRPRTPGRPL SSYGMDSRPP MAIFE LLDY IVNEPPPKLP SGVFSLEFQD FVNKCLIKNP AERADLKQLM VHAFIKRSDA EEVDFAGWLC STIGLNQPST PTHAAG VLE HHHHHHHH

UniProtKB: Dual specificity mitogen-activated protein kinase kinase 1

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Macromolecule #2: Mitogen-activated protein kinase 3

MacromoleculeName: Mitogen-activated protein kinase 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.399773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HMAAAAAQGG GGGEPRRTEG VGPGVPGEVE MVKGQPFDVG PRYTQLQYIG EGAYGMVSSA YDHVRKTRVA IKKISPFEHQ TYCQRTLRE IQILLRFRHE NVIGIRDILR ASTLEAMRDV YIVQDLMETD LYKLLKSQQL SNDHICYFLY QILRGLKYIH S ANVLHRDL ...String:
HMAAAAAQGG GGGEPRRTEG VGPGVPGEVE MVKGQPFDVG PRYTQLQYIG EGAYGMVSSA YDHVRKTRVA IKKISPFEHQ TYCQRTLRE IQILLRFRHE NVIGIRDILR ASTLEAMRDV YIVQDLMETD LYKLLKSQQL SNDHICYFLY QILRGLKYIH S ANVLHRDL KPSNLLINTT CDLKICDFGL ARIADPEHDH TGFLTEYVAT RWYRAPEIML NSKGYTKSID IWSVGCILAE ML SNRPIFP GKHYLDQLNH ILGILGSPSQ EDLNCIINMK ARNYLQSLPS KTKVAWAKLF PKSDSKALDL LDRMLTFNPN KRI TVEEAL AHPYLEQYYD PTDEPVAEEP FTFAMELDDL PKERLKELIF QETARFQPGV LEAPLEHHHH HH

UniProtKB: Mitogen-activated protein kinase 3

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 319939
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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