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- PDB-8i9j: The PKR and E3L complex -

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Basic information

Entry
Database: PDB / ID: 8i9j
TitleThe PKR and E3L complex
Components
  • (RNA-binding protein E3) x 2
  • Interferon-induced, double-stranded RNA-activated protein kinase
KeywordsVIRAL PROTEIN/TRANSFERASE / E3L / PKR / Vaccinia Virus / VIRAL PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / double-stranded RNA adenosine deaminase activity / response to interferon-alpha / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / negative regulation of osteoblast proliferation / eukaryotic translation initiation factor 2alpha kinase activity / regulation of hematopoietic progenitor cell differentiation / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of stress-activated MAPK cascade ...Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / double-stranded RNA adenosine deaminase activity / response to interferon-alpha / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / negative regulation of osteoblast proliferation / eukaryotic translation initiation factor 2alpha kinase activity / regulation of hematopoietic progenitor cell differentiation / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of stress-activated MAPK cascade / symbiont-mediated suppression of host apoptosis / symbiont-mediated evasion of host immune response / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / regulation of translational initiation / negative regulation of viral genome replication / protein serine/threonine kinase inhibitor activity / endoplasmic reticulum unfolded protein response / positive regulation of chemokine production / antiviral innate immune response / cellular response to amino acid starvation / protein sequestering activity / positive regulation of cytokine production / non-membrane spanning protein tyrosine kinase activity / Evasion by RSV of host interferon responses / non-specific protein-tyrosine kinase / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / PKR-mediated signaling / response to virus / Interferon alpha/beta signaling / kinase activity / double-stranded RNA binding / protein autophosphorylation / 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 phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / negative regulation of translation / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribosome / 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 / nucleus / membrane / 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. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Winged helix-like DNA-binding domain superfamily / 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 speciesVaccinia virus WR
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.39 Å
AuthorsHan, C.W. / Kim, H.J.
Funding support1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA-binding protein E3
A: Interferon-induced, double-stranded RNA-activated protein kinase
C: RNA-binding protein E3


Theoretical massNumber of molelcules
Total (without water)36,6633
Polymers36,6633
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA-binding protein E3 / p25


Mass: 7041.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: VACWR059, E3L / Production host: Escherichia coli (E. coli) / References: UniProt: P21605
#2: Protein Interferon-induced, double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon- ...Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon-inducible RNA-dependent protein kinase / P1/eIF-2A protein kinase / Protein kinase RNA-activated / PKR / Protein kinase R / Tyrosine-protein kinase EIF2AK2 / p68 kinase


Mass: 19705.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK2, PKR, PRKR / Production host: Escherichia coli (E. coli)
References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#3: Protein RNA-binding protein E3 / p25


Mass: 9916.187 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: VACWR059, E3L / Production host: Escherichia coli (E. coli) / References: UniProt: P21605

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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: The PKR and E3L complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.4 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 39.99 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 307424 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00814488
ELECTRON MICROSCOPYf_angle_d2.06817788
ELECTRON MICROSCOPYf_chiral_restr0.1105381
ELECTRON MICROSCOPYf_plane_restr0.0061690
ELECTRON MICROSCOPYf_dihedral_angle_d13.28361934

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