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- EMDB-17985: Cryo-EM structure of DHS-ERK2 complex with 1:3 stoichiometry refi... -

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Basic information

Entry
Database: EMDB / ID: EMD-17985
TitleCryo-EM structure of DHS-ERK2 complex with 1:3 stoichiometry refined in C1 symmetry
Map dataMain map
Sample
  • Complex: Complex of DHS-ERK2 with 1:3 stoichiometry
  • Protein or peptide: Mitogen-activated protein kinase 1
  • 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 / 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 / response to epidermal growth factor / ERKs are inactivated / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / Signaling by LTK in cancer / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytoskeleton organization / face development / androgen receptor signaling pathway / pseudopodium / RUNX2 regulates osteoblast differentiation / : / positive regulation of telomere capping / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / MAP kinase activity / RHO GTPases Activate NADPH Oxidases / regulation of ossification / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mitogen-activated protein kinase / RHO GTPases Activate WASPs and WAVEs / phosphatase binding / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Transcriptional and post-translational regulation of MITF-M expression and activity / progesterone receptor signaling pathway / Schwann cell development / Nuclear events stimulated by ALK signaling in cancer / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of T cell proliferation / stress-activated MAPK cascade / positive regulation of telomere maintenance via telomerase / phosphotyrosine residue binding / NPAS4 regulates expression of target genes / cellular response to cadmium ion / myelination / ERK1 and ERK2 cascade / cellular response to amino acid starvation / NCAM signaling for neurite out-growth / ESR-mediated signaling / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Signal transduction by L1 / Regulation of PTEN gene transcription / long-term synaptic potentiation / response to nicotine / peptidyl-threonine phosphorylation / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR3 signaling / FCERI mediated MAPK activation / B cell receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 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: 3.67 Å
AuthorsKochanowski P / Biela AP / Grudnik P
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 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

Downloads & links

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Map

FileDownload / File: emd_17985.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
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
Contour LevelBy AUTHOR: 0.284
Minimum - Maximum-1.2891645 - 2.224409
Average (Standard dev.)0.00201497 (±0.08107832)
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_17985_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map B

Fileemd_17985_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Sample components

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Entire : Complex of DHS-ERK2 with 1:3 stoichiometry

EntireName: Complex of DHS-ERK2 with 1:3 stoichiometry
Components
  • Complex: Complex of DHS-ERK2 with 1:3 stoichiometry
  • Protein or peptide: Mitogen-activated protein kinase 1
  • 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: Complex of DHS-ERK2 with 1:3 stoichiometry

SupramoleculeName: Complex of DHS-ERK2 with 1:3 stoichiometry / type: complex / ID: 1 / Parent: 0
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: Mitogen-activated protein kinase 1

MacromoleculeName: Mitogen-activated protein kinase 1 / type: protein_or_peptide / ID: 3 / 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 #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: 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 #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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Macromolecule #7: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 7 / 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
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110211
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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