[English] 日本語
Yorodumi
- PDB-8qel: PKR kinase domain- eIF2alpha in complex with compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qel
TitlePKR kinase domain- eIF2alpha in complex with compound
Components
  • Eukaryotic translation initiation factor 2 subunit alpha
  • Interferon-induced, double-stranded RNA-activated protein kinase
KeywordsRNA BINDING PROTEIN / protein synthesis/transferase / antiproliferative and antiviral effects / interferon
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 2alpha kinase activity / ABC-family proteins mediated transport / response to interferon-alpha / eukaryotic translation initiation factor 2 complex / negative regulation of osteoblast proliferation / multi-eIF complex ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 2alpha kinase activity / ABC-family proteins mediated transport / response to interferon-alpha / eukaryotic translation initiation factor 2 complex / negative regulation of osteoblast proliferation / multi-eIF complex / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of viral genome replication / antiviral innate immune response / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / translational initiation / translation initiation factor 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 / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / Interferon alpha/beta signaling / double-stranded RNA binding / ribosome binding / kinase activity / positive regulation of NF-kappaB transcription factor 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 / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / 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
Chem-UH3 / Interferon-induced, double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2 subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsNawrotek, A. / Vuillard, L. / Miallau, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PKR kinase domain- eIF2alpha in complex with compound
Authors: Nawrotek, A. / Vuillard, L. / Miallau, L.
History
DepositionAug 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2 subunit alpha
B: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2673
Polymers51,9992
Non-polymers2681
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-6 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.028, 85.028, 168.94
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 20409.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20459
#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: 31589.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TPO= phosphoarylated THR,TPO= phosphoarylated THR / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK2, PKR, PRKR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#3: Chemical ChemComp-UH3 / (3~{Z})-3-[(4-methyl-1~{H}-imidazol-5-yl)methylidene]-2-oxidanylidene-1~{H}-indole-5-carboxamide


Mass: 268.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPS pH 7.5, 10% PEG 8000, 0.2 M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.451→73.6 Å / Num. obs: 234631 / % possible obs: 89.2 % / Redundancy: 12.2 % / CC1/2: 0.99 / Net I/σ(I): 17.4
Reflection shellResolution: 2.451→2.658 Å / Num. unique obs: 10241 / CC1/2: 0.673

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.451→73.64 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.534 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.515 / SU Rfree Blow DPI: 0.315 / SU Rfree Cruickshank DPI: 0.323
RfactorNum. reflection% reflectionSelection details
Rfree0.278 942 -RANDOM
Rwork0.2412 ---
obs0.2431 19297 72.3 %-
Displacement parametersBiso mean: 80.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.3871 Å20 Å20 Å2
2---0.3871 Å20 Å2
3---0.7742 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.451→73.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 20 0 3498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073561HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924787HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1304SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes612HARMONIC5
X-RAY DIFFRACTIONt_it3561HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion458SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2516SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion20.12
LS refinement shellResolution: 2.451→2.59 Å
RfactorNum. reflection% reflection
Rfree0.4279 26 -
Rwork0.3127 --
obs--10.59 %

+
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