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- EMDB-17972: Cryo-EM structure of DHS-ERK2 complex with 1:1 stoichiometry refi... -

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Entry
Database: EMDB / ID: EMD-17972
TitleCryo-EM structure of DHS-ERK2 complex with 1:1 stoichiometry refined in C1 symmetry
Map datamain map after DeepEMhancer
Sample
  • Complex: Complex of DHS-ERK2 with 1:1 stoichiometry
    • Protein or peptide: Mitogen-activated protein kinase 1
    • Protein or peptide: Deoxyhypusine synthase
Keywordshypusination / transferase / protein-protein interaction / ERK1/2 kinase-independent function / TRANSLATION
Function / homology
Function and homology information


deoxyhypusine synthase / peptidyl-lysine modification to peptidyl-hypusine / 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 ...deoxyhypusine synthase / peptidyl-lysine modification to peptidyl-hypusine / 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 / caveolin-mediated endocytosis / cytosine metabolic process / Signaling by MAP2K mutants / Signaling by NODAL / ERKs are inactivated / response to epidermal growth factor / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / labyrinthine layer blood vessel development / ERBB signaling pathway / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / positive regulation of peptidyl-threonine phosphorylation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / MAPK1 (ERK2) activation / positive regulation of macrophage chemotaxis / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / face development / lung morphogenesis / positive regulation of telomere maintenance / Recycling pathway of L1 / pseudopodium / Bergmann glial cell differentiation / androgen receptor signaling pathway / thyroid gland development / steroid hormone receptor signaling pathway / Advanced glycosylation endproduct receptor signaling / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / negative regulation of cell differentiation / regulation of ossification / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate WASPs and WAVEs / JUN kinase activity / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / phosphatase binding / Schwann cell development / Growth hormone receptor signaling / progesterone receptor signaling pathway / positive regulation of T cell proliferation / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / ERK1 and ERK2 cascade / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ESR-mediated signaling / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to nicotine / 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 / positive regulation of cholesterol biosynthetic process / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKochanowski P / Biela AP / Grudnik P
Funding support Poland, 3 items
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, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17972.png

Downloads & links

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Map

FileDownload / File: emd_17972.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map after DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.0016886787 - 1.8318133
Average (Standard dev.)0.00028107452 (±0.03563873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_17972_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_17972_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of DHS-ERK2 with 1:1 stoichiometry

EntireName: Complex of DHS-ERK2 with 1:1 stoichiometry
Components
  • Complex: Complex of DHS-ERK2 with 1:1 stoichiometry
    • Protein or peptide: Mitogen-activated protein kinase 1
    • Protein or peptide: Deoxyhypusine synthase

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Supramolecule #1: Complex of DHS-ERK2 with 1:1 stoichiometry

SupramoleculeName: Complex of DHS-ERK2 with 1:1 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitogen-activated protein kinase 1

MacromoleculeName: Mitogen-activated protein kinase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.53173 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMAAAAAAGA GPEMVRGQVF DVGPRYTNLS YIGEGAYGMV CSAYDNVNKV RVAIKKISPF EHQTYCQRTL REIKILLRFR HENIIGIND IIRAPTIEQM KDVYIVQDLM ETDLYKLLKT QHLSNDHICY FLYQILRGLK YIHSANVLHR DLKPSNLLLN T TCDLKICD ...String:
SMAAAAAAGA GPEMVRGQVF DVGPRYTNLS YIGEGAYGMV CSAYDNVNKV RVAIKKISPF EHQTYCQRTL REIKILLRFR HENIIGIND IIRAPTIEQM KDVYIVQDLM ETDLYKLLKT QHLSNDHICY FLYQILRGLK YIHSANVLHR DLKPSNLLLN T TCDLKICD FGLARVADPD HDHTGFLTEY VATRWYRAPE IMLNSKGYTK SIDIWSVGCI LAEMLSNRPI FPGKHYLDQL NH ILGILGS PSQEDLNCII NLKARNYLLS LPHKNKVPWN RLFPNADSKA LDLLDKMLTF NPHKRIEVEQ ALAHPYLEQY YDP SDEPIA EAPFKFDMEL DDLPKEKLKE LIFEETARFQ PGYRS

UniProtKB: Mitogen-activated protein kinase 1

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Macromolecule #2: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.099512 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLT QSRRPLTSCT IFLGYTSNLI SSGIRETIRY LVQHNMVDVL VTTAGGVEED LIKCLAPTYL GEFSLRGKEL R ENGINRIG ...String:
SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLT QSRRPLTSCT IFLGYTSNLI SSGIRETIRY LVQHNMVDVL VTTAGGVEED LIKCLAPTYL GEFSLRGKEL R ENGINRIG NLLVPNENYC KFEDWLMPIL DQMVMEQNTE GVKWTPSKMI ARLGKEINNP ESVYYWAQKN HIPVFSPALT DG SLGDMIF FHSYKNPGLV LDIVEDLRLI NTQAIFAKCT GMIILGGGVV KHHIANANLM RNGADYAVYI NTAQEFDGSD SGA RPDEAV SWGKIRVDAQ PVKVYADASL VFPLLVAETF AQKMDAFMHE KNED

UniProtKB: Deoxyhypusine synthase

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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

Concentration0.35 mg/mL
BufferpH: 7.8 / Details: 50mM Tris-HCl, 200mM NaCl, 3mM 2-mercaptoethanol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: blot time: 2 s, blot force: 0.
DetailsComplex was stabilized with bis(sulfosuccinimidyl)suberate

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6930 / Average electron dose: 40.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsmotion corrected in Relion and further processed in cryoSPARC
Particle selectionNumber selected: 438 / Details: Manually picked
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 146572
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Avg.num./class: 70637 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8a0e

chain_id: A, source_name: PDB, initial_model_type: experimental model

8a0e

chain_id: B, source_name: PDB, initial_model_type: experimental model

8a0e

chain_id: C, source_name: PDB, initial_model_type: experimental model

8a0e

chain_id: D, source_name: PDB, initial_model_type: experimental model

4qta

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8pvu:
Cryo-EM structure of DHS-ERK2 complex with 1:1 stoichiometry refined in C1 symmetry

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