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- EMDB-35274: The PKR and E3L complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35274
TitleThe PKR and E3L complex
Map data
Sample
  • Complex: The PKR and E3L complex
    • Protein or peptide: RNA-binding protein E3
    • Protein or peptide: Interferon-induced, double-stranded RNA-activated protein kinase
    • Protein or peptide: RNA-binding protein E3
KeywordsE3L / PKR / Vaccinia Virus / VIRAL PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / double-stranded RNA adenosine deaminase activity / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / suppression by virus of host type I interferon production / negative regulation of osteoblast proliferation / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated perturbation of host apoptosis ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / double-stranded RNA adenosine deaminase activity / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / suppression by virus of host type I interferon production / negative regulation of osteoblast proliferation / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated perturbation of host apoptosis / regulation of hematopoietic progenitor cell differentiation / symbiont-mediated suppression of host apoptosis / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / evasion of host immune response / SUMOylation of immune response proteins / regulation of hematopoietic stem cell differentiation / regulation of hematopoietic stem cell proliferation / protein serine/threonine kinase inhibitor activity / negative regulation of viral genome replication / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / antiviral innate immune response / protein sequestering activity / cellular response to amino acid starvation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / double-stranded RNA binding / Interferon alpha/beta signaling / kinase activity / positive regulation of NF-kappaB transcription factor activity / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / defense response to virus / protein autophosphorylation / positive regulation of MAPK cascade / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribosome / protein phosphorylation / translation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein E3 / EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Protein E3 / EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix DNA-binding domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Winged helix-like DNA-binding domain superfamily / 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
Interferon-induced, double-stranded RNA-activated protein kinase / RNA-binding protein OPG065
Similarity search - Component
Biological speciesHomo sapiens (human) / Vaccinia virus WR
Methodsingle particle reconstruction / cryo EM / Resolution: 6.39 Å
AuthorsHan CW / Kim HJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Biophys Res Commun / Year: 2023
Title: Structural study of novel vaccinia virus E3L and dsRNA-dependent protein kinase complex.
Authors: Hyeon Jin Kim / Chang Woo Han / Mi Suk Jeong / Se Bok Jang /
Abstract: E3L (RNA-binding protein E3) is one of the key IFN resistance genes encoded by VV and consists of 190 amino acids with a highly conserved carboxy-terminal double-stranded RNA-binding domain (dsRBD). ...E3L (RNA-binding protein E3) is one of the key IFN resistance genes encoded by VV and consists of 190 amino acids with a highly conserved carboxy-terminal double-stranded RNA-binding domain (dsRBD). PKR (dsRNA-dependent protein kinase) is an IFN-induced protein involved in anti-cell and antiviral activity. PKR inhibits the initiation of translation through alpha subunit of the initiation factor eIF2 (eIF2α) and mediates several transcription factors such as NF-κB, p53 or STATs. Activated PKR also induces apoptosis in vaccinia virus infection. E3L is required for viral IFN resistance and directly binds to PKR to block activation of PKR. In this work, we determined the three-dimensional complex structure of E3L and PKR using cryo-EM and determined the important residues involved in the interaction. In addition, PKR peptide binds to E3L and can increase protein levels of phosphorus-PKR and phosphorus-eIF2α-induced cell apoptosis through upregulation of phosphorus-PKR in HEK293 cells. Taken together, structural insights into E3L and PKR will provide a new optimization and development of vaccinia virus drugs.
History
DepositionFeb 7, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35274.png

Downloads & links

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Map

FileDownload / File: emd_35274.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 256 pix.
= 292.864 Å		1.14 Å/pix.
x 256 pix.
= 292.864 Å		1.14 Å/pix.
x 256 pix.
= 292.864 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.144 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.4231099 - 0.70256084
Average (Standard dev.)0.00031016962 (±0.028001364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 292.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_35274_additional_1.map
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Half map: #2

Fileemd_35274_half_map_1.map
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Half map: #1

Fileemd_35274_half_map_2.map
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Sample components

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Entire : The PKR and E3L complex

EntireName: The PKR and E3L complex
Components
  • Complex: The PKR and E3L complex
    • Protein or peptide: RNA-binding protein E3
    • Protein or peptide: Interferon-induced, double-stranded RNA-activated protein kinase
    • Protein or peptide: RNA-binding protein E3

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Supramolecule #1: The PKR and E3L complex

SupramoleculeName: The PKR and E3L complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: RNA-binding protein E3

MacromoleculeName: RNA-binding protein E3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR / Strain: Western Reserve
Molecular weightTheoretical: 7.041031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSNAEIVCEA IKTIGIEGAT AAQLTRQLNM EKREVNKALY DLQRSAMVYS SDDIPPRWFM TT

UniProtKB: RNA-binding protein OPG065

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Macromolecule #2: Interferon-induced, double-stranded RNA-activated protein kinase

MacromoleculeName: Interferon-induced, double-stranded RNA-activated protein kinase
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.705418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMEMAGDL SAGFFMEELN TYRQKQGVVL KYQELPNSGP PHDRRFTFQV IIDGREFPEG EGRSKKEAKN AAAKLAVEIL NKEKKAVSP LLLTTTNSSE GLSMGNYIGL INRIAQKKRL TVNYEQCASG VHGPEGFHYK CKMGQKEYSI GTGSTKQEAK Q LAAKLAYL QILSEETGSG C

UniProtKB: Interferon-induced, double-stranded RNA-activated protein kinase

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Macromolecule #3: RNA-binding protein E3

MacromoleculeName: RNA-binding protein E3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR / Strain: Western Reserve
Molecular weightTheoretical: 9.916187 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EDHKSFDDVI PAKKIIDWKG ANPVTVINEY CQITRRDWSF RIESVGPSNS PTFYACVDID GRVFDKADGK SKRDAKNNAA KLAVDKLL

UniProtKB: RNA-binding protein OPG065

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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

BufferpH: 7.1
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.99 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1oyi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307424
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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