[English] 日本語
Yorodumi
- PDB-8i9j: The PKR and E3L complex -

+
Open data


ID or keywords:

Loading...

-
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


: / 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 ...: / 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 / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / antiviral innate immune response / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / 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 / positive regulation of MAPK cascade / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / translation / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytoplasm / cytosol
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 profile. / Z-binding domain / Adenosine deaminase z-alpha domain / 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 profile. / Z-binding domain / Adenosine deaminase z-alpha domain / 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 / Protein E3
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more