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- PDB-8qel: PKR kinase domain- eIF2alpha in complex with compound -

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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


Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / response to interferon-alpha / ABC-family proteins mediated transport / negative regulation of osteoblast proliferation / eukaryotic translation initiation factor 2 complex / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade ...Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / response to interferon-alpha / ABC-family proteins mediated transport / negative regulation of osteoblast proliferation / eukaryotic translation initiation factor 2 complex / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / multi-eIF complex / 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 translational initiation / regulation of hematopoietic stem cell differentiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / negative regulation of viral genome replication / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / endoplasmic reticulum unfolded protein response / positive regulation of chemokine production / antiviral innate immune response / translation initiation factor activity / cellular response to amino acid starvation / positive regulation of cytokine production / non-membrane spanning protein tyrosine kinase activity / translational initiation / non-specific protein-tyrosine kinase / positive regulation of non-canonical NF-kappaB signal transduction / PKR-mediated signaling / Evasion by RSV of host interferon responses / response to virus / ISG15 antiviral mechanism / cytoplasmic stress granule / positive regulation of NF-kappaB transcription factor activity / Interferon alpha/beta signaling / kinase activity / double-stranded RNA binding / ribosome binding / protein autophosphorylation / defense response to virus / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / negative regulation of translation / 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 / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Translation initiation factor 2; subunit 1; domain 2 / : / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Double-stranded RNA binding motif ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Translation initiation factor 2; subunit 1; domain 2 / : / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / 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 / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
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
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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 %

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