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- PDB-6d3l: Crystal structure of unphosphorylated human PKR -

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Basic information

Entry
Database: PDB / ID: 6d3l
TitleCrystal structure of unphosphorylated human PKR
ComponentsInterferon-induced, double-stranded RNA-activated protein kinase
KeywordsTRANSFERASE / unphosphorylated / kinase / activation loop swapping / apo
Function / homology
Function and homology information


Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / response to interferon-alpha / negative regulation of osteoblast proliferation / 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 translational initiation ...Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / response to interferon-alpha / negative regulation of osteoblast proliferation / 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 translational initiation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / endoplasmic reticulum unfolded protein response / positive regulation of chemokine production / antiviral innate immune response / cellular response to amino acid starvation / positive regulation of cytokine production / non-membrane spanning protein tyrosine kinase activity / 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 / positive regulation of NF-kappaB transcription factor activity / Interferon alpha/beta signaling / kinase activity / double-stranded RNA 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 / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsErlandsen, H. / Mayo, C. / Robinson, V.L. / Cole, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI053615 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural Basis of Protein Kinase R Autophosphorylation.
Authors: Mayo, C.B. / Erlandsen, H. / Mouser, D.J. / Feinstein, A.G. / Robinson, V.L. / May, E.R. / Cole, J.L.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Interferon-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)37,4461
Polymers37,4461
Non-polymers00
Water00
1
A: Interferon-induced, double-stranded RNA-activated protein kinase

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


  • defined by author
  • Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of ...Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of Molecular Biology, 345(1), 81-90. http://doi.org/10.1016/j.jmb.2004.10.031
  • 74.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)74,8922
Polymers74,8922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
2
A: Interferon-induced, double-stranded RNA-activated protein kinase

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


  • defined by author
  • Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of ...Evidence: equilibrium centrifugation, Lemaire, P. A., Lary, J., & Cole, J. L. (2005). Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. Journal of Molecular Biology, 345(1), 81-90. http://doi.org/10.1016/j.jmb.2004.10.031, fluorescence resonance energy transfer, Husain, B., Hesler, S., & Cole, J. L. (2015). Regulation of PKR by RNA: Formation of Active and Inactive Dimers. Biochemistry, 54(44), 6663-6672. http://doi.org/10.1021/acs.biochem.5b01046
  • 74.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)74,8922
Polymers74,8922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Unit cell
Length a, b, c (Å)92.689, 92.689, 123.325
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: 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 / Protein kinase R / Tyrosine-protein kinase EIF2AK2 / p68 kinase


Mass: 37445.773 Da / Num. of mol.: 1 / Fragment: kinase domain (229-551)
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

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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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 2.0 M ammonium sulfate, 1:3 molar ratio of dp8 (heparin) was added to protein prior to crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.978971 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978971 Å / Relative weight: 1
ReflectionResolution: 3.1→123.33 Å / Num. obs: 6130 / % possible obs: 100 % / Redundancy: 17.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.063 / Rrim(I) all: 0.267 / Net I/σ(I): 9.1
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.133 / Num. unique obs: 1065 / CC1/2: 0.677 / Rpim(I) all: 0.263 / Rrim(I) all: 1.163 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.04 Å80.27 Å
Translation6.04 Å80.27 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.28data scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A19

2a19


Resolution: 3.1→123.33 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.812 / SU B: 34.802 / SU ML: 0.573 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.65 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.347 296 4.9 %RANDOM
Rwork0.2585 ---
obs0.2629 5801 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.27 Å2 / Biso mean: 88.324 Å2 / Biso min: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 3.1→123.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 0 0 2014
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192082
X-RAY DIFFRACTIONr_bond_other_d0.0020.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9692793
X-RAY DIFFRACTIONr_angle_other_deg1.01634720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.56624.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1541511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
LS refinement shellResolution: 3.1→3.181 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 16 -
Rwork0.383 410 -
all-426 -
obs--100 %

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