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- EMDB-17981: Cryo-EM structure of the second of three possible DHS-ERK2 comple... -

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Entry
Database: EMDB / ID: EMD-17981
TitleCryo-EM structure of the second of three possible DHS-ERK2 complexes with 1:2 stoichiometry refined in C1 symmetry
Map dataMain map
Sample
  • Complex: One of three possible DHS-ERK2 complexes with 1:2 stoichiometry refined in C1 symmetry
    • Protein or peptide: Mitogen-activated protein kinase 1
    • Protein or peptide: Mitogen-activated protein kinase 1
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
Keywordshypusination / transferase / protein-protein interaction / ERK1/2 kinase-independent function / TRANSLATION
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 / cytosine metabolic process / cardiac neural crest cell development involved in heart development / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / RSK activation / ERKs are inactivated / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / outer ear morphogenesis / : / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / Signaling by LTK in cancer / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / ERBB signaling pathway / trachea formation / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / positive regulation of neuroinflammatory response / Frs2-mediated activation / Activation of the AP-1 family of transcription factors / ERBB2-ERBB3 signaling pathway / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / ERK/MAPK targets / MAPK1 (ERK2) activation / regulation of cytoskeleton organization / positive regulation of macrophage chemotaxis / face development / Bergmann glial cell differentiation / Recycling pathway of L1 / thyroid gland development / positive regulation of telomere maintenance / pseudopodium / lung morphogenesis / Advanced glycosylation endproduct receptor signaling / 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 / negative regulation of cell differentiation / Signal attenuation / RHO GTPases Activate WASPs and WAVEs / Growth hormone receptor signaling / Schwann cell development / stress-activated MAPK cascade / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / Nuclear events stimulated by ALK signaling in cancer / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / positive regulation of T cell proliferation / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ciliary tip / thymus development / cellular response to amino acid starvation / Regulation of PTEN gene transcription / chemokine-mediated signaling pathway / Signal transduction by L1 / B cell receptor signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / protein maturation / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / positive regulation of cholesterol biosynthetic process
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: 3.82 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-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17981.png

Downloads & links

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Map

FileDownload / File: emd_17981.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
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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: 0.219
Minimum - Maximum-0.88405144 - 1.5233746
Average (Standard dev.)0.0011835082 (±0.06266242)
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 B

Fileemd_17981_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_17981_half_map_2.map
AnnotationHalf map A
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : One of three possible DHS-ERK2 complexes with 1:2 stoichiometry r...

EntireName: One of three possible DHS-ERK2 complexes with 1:2 stoichiometry refined in C1 symmetry
Components
  • Complex: One of three possible DHS-ERK2 complexes with 1:2 stoichiometry refined in C1 symmetry
    • Protein or peptide: Mitogen-activated protein kinase 1
    • Protein or peptide: Mitogen-activated protein kinase 1
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase

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Supramolecule #1: One of three possible DHS-ERK2 complexes with 1:2 stoichiometry r...

SupramoleculeName: One of three possible DHS-ERK2 complexes with 1:2 stoichiometry refined in C1 symmetry
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 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMAAAAAAGA GPEMVRGQVF DVGPRYTNLS YIGEGAYGMV CSAYDNVNKV RVAIKKISPF EHQTYCQRTL REIKILLRFR HENIIGINDI IRAPTIEQMK DVYIVQDLME TDLYKLLKTQ HLSNDHICYF LYQILRGLKY IHSANVLHRD LKPSNLLLNT TCDLKICDFG ...String:
SMAAAAAAGA GPEMVRGQVF DVGPRYTNLS YIGEGAYGMV CSAYDNVNKV RVAIKKISPF EHQTYCQRTL REIKILLRFR HENIIGINDI IRAPTIEQMK DVYIVQDLME TDLYKLLKTQ HLSNDHICYF LYQILRGLKY IHSANVLHRD LKPSNLLLNT TCDLKICDFG LARVADPDHD HTGFLTEYVA TRWYRAPEIM LNSKGYTKSI DIWSVGCILA EMLSNRPIFP GKHYLDQLNH ILGILGSPSQ EDLNCIINLK ARNYLLSLPH KNKVPWNRLF PNADSKALDL LDKMLTFNPH KRIEVEQALA HPYLEQYYDP SDEPIAEAPF KFDMELDDLP KEKLKELIFE ETARFQPGYR S

UniProtKB: Mitogen-activated protein kinase 1

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Macromolecule #2: Mitogen-activated protein kinase 1

MacromoleculeName: Mitogen-activated protein kinase 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMAAAAAAGA GPEMVRGQVF DVGPRYTNLS YIGEGAYGMV CSAYDNVNKV RVAIKKISPF EHQTYCQRTL REIKILLRFR HENIIGINDI IRAPTIEQMK DVYIVQDLME TDLYKLLKTQ HLSNDHICYF LYQILRGLKY IHSANVLHRD LKPSNLLLNT TCDLKICDFG ...String:
SMAAAAAAGA GPEMVRGQVF DVGPRYTNLS YIGEGAYGMV CSAYDNVNKV RVAIKKISPF EHQTYCQRTL REIKILLRFR HENIIGINDI IRAPTIEQMK DVYIVQDLME TDLYKLLKTQ HLSNDHICYF LYQILRGLKY IHSANVLHRD LKPSNLLLNT TCDLKICDFG LARVADPDHD HTGFLTEYVA TRWYRAPEIM LNSKGYTKSI DIWSVGCILA EMLSNRPIFP GKHYLDQLNH ILGILGSPSQ EDLNCIINLK ARNYLLSLPH KNKVPWNRLF PNADSKALDL LDKMLTFNPH KRIEVEQALA HPYLEQYYDP SDEPIAEAPF KFDMELDDLP KEKLKELIFE ETARFQPGYR S

UniProtKB: Mitogen-activated protein kinase 1

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Macromolecule #3: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL ...String:
SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL LVPNENYCKF EDWLMPILDQ MVMEQNTEGV KWTPSKMIAR LGKEINNPES VYYWAQKNHI PVFSPALTDG SLGDMIFFHS YKNPGLVLDI VEDLRLINTQ AIFAKCTGMI ILGGGVVKHH IANANLMRNG ADYAVYINTA QEFDGSDSGA RPDEAVSWGK IRVDAQPVKV YADASLVFPL LVAETFAQKM DAFMHEKNED

UniProtKB: Deoxyhypusine synthase

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Macromolecule #4: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL ...String:
SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL LVPNENYCKF EDWLMPILDQ MVMEQNTEGV KWTPSKMIAR LGKEINNPES VYYWAQKNHI PVFSPALTDG SLGDMIFFHS YKNPGLVLDI VEDLRLINTQ AIFAKCTGMI ILGGGVVKHH IANANLMRNG ADYAVYINTA QEFDGSDSGA RPDEAVSWGK IRVDAQPVKV YADASLVFPL LVAETFAQKM DAFMHEKNED

UniProtKB: Deoxyhypusine synthase

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Macromolecule #5: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 5 / Enantiomer: DEXTRO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL ...String:
SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL LVPNENYCKF EDWLMPILDQ MVMEQNTEGV KWTPSKMIAR LGKEINNPES VYYWAQKNHI PVFSPALTDG SLGDMIFFHS YKNPGLVLDI VEDLRLINTQ AIFAKCTGMI ILGGGVVKHH IANANLMRNG ADYAVYINTA QEFDGSDSGA RPDEAVSWGK IRVDAQPVKV YADASLVFPL LVAETFAQKM DAFMHEKNED

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Macromolecule #6: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL ...String:
SMEGSLEREA PAGALAAVLK HSSTLPPEST QVRGYDFNRG VNYRALLEAF GTTGFQATNF GRAVQQVNAM IEKKLEPLSQ DEDQHADLTQ SRRPLTSCTI FLGYTSNLIS SGIRETIRYL VQHNMVDVLV TTAGGVEEDL IKCLAPTYLG EFSLRGKELR ENGINRIGNL LVPNENYCKF EDWLMPILDQ MVMEQNTEGV KWTPSKMIAR LGKEINNPES VYYWAQKNHI PVFSPALTDG SLGDMIFFHS YKNPGLVLDI VEDLRLINTQ AIFAKCTGMI ILGGGVVKHH IANANLMRNG ADYAVYINTA QEFDGSDSGA RPDEAVSWGK IRVDAQPVKV YADASLVFPL LVAETFAQKM DAFMHEKNED

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
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100840
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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