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- PDB-8pvu: Cryo-EM structure of DHS-ERK2 complex with 1:1 stoichiometry refi... -

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Basic information

Entry
Database: PDB / ID: 8pvu
TitleCryo-EM structure of DHS-ERK2 complex with 1:1 stoichiometry refined in C1 symmetry
Components
  • Deoxyhypusine synthase
  • Mitogen-activated protein kinase 1
KeywordsTRANSLATION / hypusination / transferase / protein-protein interaction / ERK1/2 kinase-independent function
Function / homology
Function and homology information


deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK ...deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / phospho-PLA2 pathway / Signaling by MAPK mutants / 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 / cytosine metabolic process / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / outer ear morphogenesis / trachea formation / labyrinthine layer blood vessel development / response to epidermal growth factor / Signaling by NODAL / RSK activation / Signaling by MAP2K mutants / ERKs are inactivated / Bergmann glial cell differentiation / lung morphogenesis / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / : / mammary gland epithelial cell proliferation / regulation of Golgi inheritance / Signaling by LTK in cancer / positive regulation of peptidyl-threonine phosphorylation / face development / ERBB signaling pathway / regulation of early endosome to late endosome transport / thyroid gland development / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / positive regulation of neuroinflammatory response / IFNG signaling activates MAPKs / Frs2-mediated activation / response to exogenous dsRNA / Activation of the AP-1 family of transcription factors / ERBB2-ERBB3 signaling pathway / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / regulation of cytoskeleton organization / positive regulation of macrophage chemotaxis / MAPK1 (ERK2) activation / Recycling pathway of L1 / pseudopodium / positive regulation of telomere maintenance / regulation of ossification / MAP kinase activity / Advanced glycosylation endproduct receptor signaling / mitogen-activated protein kinase / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / stress-activated MAPK cascade / ERK1 and ERK2 cascade / RHO GTPases Activate NADPH Oxidases / Signal attenuation / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / Growth hormone receptor signaling / Schwann cell development / thymus development / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / myelination / NPAS4 regulates expression of target genes / lipopolysaccharide-mediated signaling pathway / phosphotyrosine residue binding / insulin-like growth factor receptor signaling pathway / ciliary tip / Nuclear events stimulated by ALK signaling in cancer / RNA polymerase II CTD heptapeptide repeat kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / ESR-mediated signaling / NCAM signaling for neurite out-growth / cellular response to amino acid starvation / B cell receptor signaling pathway / Regulation of PTEN gene transcription / Signal transduction by L1 / chemokine-mediated signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / protein maturation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / cellular response to tumor necrosis factor / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Signaling by high-kinase activity BRAF mutants / positive regulation of cholesterol biosynthetic process / Spry regulation of FGF signaling
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / Mitogen-activated protein (MAP) kinase, ERK1/2 / DHS-like NAD/FAD-binding domain superfamily / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / Mitogen-activated protein (MAP) kinase, ERK1/2 / DHS-like NAD/FAD-binding domain superfamily / 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 1 / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKochanowski, P. / Biela, A.P. / Grudnik, P.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 Poland
Polish National Science CentreUMO-2022/47/B/NZ7/01667 Poland
Polish National Science CentreUMO-2023/49/N/NZ1/03559 Poland
CitationJournal: Cell Rep / Year: 2024
Title: ERK1/2 interaction with DHPS regulates eIF5A deoxyhypusination independently of ERK kinase activity.
Authors: Andrew E Becker / Paweł Kochanowski / Pui-Kei Wu / Elżbieta Wątor / Wenjing Chen / Koushik Guchhait / Artur P Biela / Przemysław Grudnik / Jong-In Park /
Abstract: This study explores a non-kinase effect of extracellular regulated kinases 1/2 (ERK1/2) on the interaction between deoxyhypusine synthase (DHPS) and its substrate, eukaryotic translation initiation ...This study explores a non-kinase effect of extracellular regulated kinases 1/2 (ERK1/2) on the interaction between deoxyhypusine synthase (DHPS) and its substrate, eukaryotic translation initiation factor 5A (eIF5A). We report that Raf/MEK/ERK activation decreases the DHPS-ERK1/2 interaction while increasing DHPS-eIF5A association in cells. We determined the cryoelectron microscopy (cryo-EM) structure of the DHPS-ERK2 complex at 3.5 Å to show that ERK2 hinders substrate entrance to the DHPS active site, subsequently inhibiting deoxyhypusination in vitro. In cells, impairing the ERK2 activation loop, but not the catalytic site, prolongs the DHPS-ERK2 interaction irrespective of Raf/MEK signaling. The ERK2 Ser-Pro-Ser motif, but not the common docking or F-site recognition sites, also regulates this complex. These data suggest that ERK1/2 dynamically regulate the DHPS-eIF5A interaction in response to Raf/MEK activity, regardless of its kinase function. In contrast, ERK1/2 kinase activity is necessary to regulate the expression of DHPS and eIF5A. These findings highlight an ERK1/2-mediated dual kinase-dependent and -independent regulation of deoxyhypusination.
History
DepositionJul 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
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Revision 1.1Oct 23, 2024Group: Author supporting evidence / Data collection / Database references
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Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Mar 4, 2026Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.1Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Mitogen-activated protein kinase 1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
C: Deoxyhypusine synthase
D: Deoxyhypusine synthase


Theoretical massNumber of molelcules
Total (without water)205,9305
Polymers205,9305
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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: 41531.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Protein
Deoxyhypusine synthase / DHS


Mass: 41099.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase
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

ComponentName: Complex of DHS-ERK2 with 1:1 stoichiometry / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8 / Details: 50mM Tris-HCl, 200mM NaCl, 3mM 2-mercaptoethanol
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Complex was stabilized with bis(sulfosuccinimidyl)suberate
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K / Details: blot time: 2 s, blot force: 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40.16 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6930
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU2.10.0.1941RELimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
Image processingDetails: motion corrected in Relion and further processed in cryoSPARC
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 438 / Details: Manually picked
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146572 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
18A0E

8a0e

A8A0EA1
28A0E

8a0e

B8A0EB1
38A0E

8a0e

C8A0EC1
48A0E

8a0e

D8A0ED1
54QTA

4qta

A4QTAA2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412570
ELECTRON MICROSCOPYf_angle_d0.56517031
ELECTRON MICROSCOPYf_dihedral_angle_d3.8551677
ELECTRON MICROSCOPYf_chiral_restr0.0441916
ELECTRON MICROSCOPYf_plane_restr0.0052192

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