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- PDB-9tu0: Crystal structure of human ERK1 in complex with the KIM1 motif of... -

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Basic information

Entry
Database: PDB / ID: 9tu0
TitleCrystal structure of human ERK1 in complex with the KIM1 motif of the T. gondii protein GRA24
Components
  • Mitogen-activated protein kinase 3
  • Putative transmembrane protein
KeywordsTRANSFERASE / phosphoryl transfer / kinase / MAPK / GRA24 / toxoplasma
Function / homology
Function and homology information


negative regulation of cholesterol efflux / positive regulation of xenophagy / xenophagy / negative regulation of T cell mediated immune response to tumor cell / interleukin-34-mediated signaling pathway / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development ...negative regulation of cholesterol efflux / positive regulation of xenophagy / xenophagy / negative regulation of T cell mediated immune response to tumor cell / interleukin-34-mediated signaling pathway / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / ERKs are inactivated / RSK activation / positive regulation of cyclase activity / phosphorylation / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / cartilage development / Signaling by LTK in cancer / regulation of Golgi inheritance / positive regulation of neuroinflammatory response / interleukin-1-mediated signaling pathway / peptidyl-tyrosine autophosphorylation / trachea formation / 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 / ERK/MAPK targets / ciliary tip / response to exogenous dsRNA / positive regulation of macrophage chemotaxis / face development / pseudopodium / Bergmann glial cell differentiation / lung morphogenesis / positive regulation of telomere maintenance / thyroid gland development / Advanced glycosylation endproduct receptor signaling / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / RHO GTPases Activate NADPH Oxidases / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / Signal attenuation / Growth hormone receptor signaling / BMP signaling pathway / Schwann cell development / phosphatase binding / stress-activated MAPK cascade / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / negative regulation of TORC1 signaling / myelination / NCAM signaling for neurite out-growth / Transcriptional and post-translational regulation of MITF-M expression and activity / sensory perception of pain / insulin-like growth factor receptor signaling pathway / ESR-mediated signaling / RNA Polymerase I Promoter Opening / lipopolysaccharide-mediated signaling pathway / cellular response to amino acid starvation / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative Regulation of CDH1 Gene Transcription / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / cellular response to mechanical stimulus / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Oncogene Induced Senescence / caveola / Regulation of actin dynamics for phagocytic cup formation / modulation of chemical synaptic transmission / ISG15 antiviral mechanism
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 / Protein kinases ATP-binding region signature. ...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
Putative transmembrane protein / Mitogen-activated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsJuyoux, P. / von Velsen, J. / 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: Jill von Velsen / Pauline Juyoux / Nicola Piasentin / Hayden Fisher / Karine Lapouge / Oscar Vadas / Francesco Luigi Gervasio / Matthew W Bowler /
Abstract: The RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) pathway relays extracellular signals into a cellular response and its dysregulation leads to many pathologies, particularly cancer. Here, ...The RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) pathway relays extracellular signals into a cellular response and its dysregulation leads to many pathologies, particularly cancer. Here, we determined cryo-EM structures of the MAP2K MEK1 activating its substrate MAPK ERK2, the final event in the cascade. We define the molecular details of specificity and phosphoryl transfer to the tyrosine of the ERK2 activation loop and examine the mechanism of substrate recognition using solution techniques and molecular dynamics. Binding of the substrate MAPK leads to release of the MAP2K catalytic machinery, explaining the mechanism of many disease-causing mutations, and ERK2 release is not required for nucleotide exchange, suggesting a processive mechanism. Our data advance the understanding of MAPK signalling and provide a starting point for drug development.
History
DepositionJan 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 3
D: Putative transmembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9615
Polymers100,6732
Non-polymers2883
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-37 kcal/mol
Surface area17330 Å2
Unit cell
Length a, b, c (Å)59.817, 59.817, 388.698
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Mitogen-activated protein kinase 3 / MAP kinase 3 / MAPK 3 / ERT2 / Extracellular signal-regulated kinase 1 / ERK-1 / Insulin-stimulated ...MAP kinase 3 / MAPK 3 / ERT2 / Extracellular signal-regulated kinase 1 / ERK-1 / Insulin-stimulated MAP2 kinase / MAP kinase isoform p44 / p44-MAPK / Microtubule-associated protein 2 kinase / p44-ERK1


Mass: 43270.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK3, ERK1, PRKM3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P27361, mitogen-activated protein kinase
#2: Protein Putative transmembrane protein


Mass: 57402.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote) / References: UniProt: B6KJB6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.34 % / Description: crystal volume: 0.107 x 0.079 x 0.101 mm3
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MES pH 7, 10% dioxane and 1.8 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 6, 2018 / Details: Be CRL
RadiationMonochromator: C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.17→64.7 Å / Num. obs: 609516 / % possible obs: 91.6 % / Redundancy: 34 % / Biso Wilson estimate: 42.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.032 / Rrim(I) all: 0.186 / Net I/σ(I): 18.5
Reflection shellResolution: 2.17→2.38 Å / Redundancy: 36.1 % / Rmerge(I) obs: 2.649 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 32486 / CC1/2: 0.919 / Rpim(I) all: 0.442 / Rrim(I) all: 2.687 / % possible all: 49

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→19.93 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.292 881 4.99 %
Rwork0.237 16773 -
obs0.2399 17654 76.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.22 Å2
Refinement stepCycle: LAST / Resolution: 2.17→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 15 70 2894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232881
X-RAY DIFFRACTIONf_angle_d0.55153899
X-RAY DIFFRACTIONf_chiral_restr0.0408431
X-RAY DIFFRACTIONf_plane_restr0.0043494
X-RAY DIFFRACTIONf_dihedral_angle_d15.99281100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.311.0639130.4131345X-RAY DIFFRACTION9.54
2.31-2.480.37611030.33291666X-RAY DIFFRACTION47.19
2.48-2.730.38051790.31263594X-RAY DIFFRACTION99.6
2.73-3.130.33971960.28773602X-RAY DIFFRACTION100
3.13-3.940.35451770.25333580X-RAY DIFFRACTION96.43
3.94-19.930.21462130.1853986X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.8602585356 Å / Origin y: 16.8996154895 Å / Origin z: -15.1108364711 Å
111213212223313233
T0.0971823903311 Å2-0.0878189578942 Å20.0455129294694 Å2-0.251389847283 Å2-0.109347916171 Å2--0.144503813182 Å2
L1.93630459426 °2-0.509348948835 °2-0.412792287481 °2-0.855527523824 °20.541949077173 °2--1.16427987708 °2
S-0.104654117905 Å °-0.0653048139691 Å °-0.0893596671174 Å °-0.0842024996551 Å °0.0555511904028 Å °0.034307570615 Å °-0.0342522848736 Å °-0.00166374883683 Å °0.0303650626594 Å °
Refinement TLS groupSelection details: all

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