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- PDB-2a1a: PKR kinase domain-eIF2alpha Complex -

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Basic information

Entry
Database: PDB / ID: 2a1a
TitlePKR kinase domain-eIF2alpha Complex
Components
  • Eukaryotic translation initiation factor 2 alpha subunit
  • Interferon-induced, double-stranded RNA-activated protein kinase
Keywordsprotein synthesis/transferase / transferase / kinase / protein biosynthesis / protein synthesis-transferase COMPLEX
Function / homology
Function and homology information


Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2alpha kinase activity / 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 ...Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2alpha kinase activity / 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 / formation of translation preinitiation complex / protein phosphatase regulator activity / eukaryotic 48S preinitiation complex / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / regulation of translational initiation / 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 / translation initiation factor activity / 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 / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / response to virus / cytoplasmic stress granule / Interferon alpha/beta signaling / kinase activity / double-stranded RNA binding / ribosome binding / protein autophosphorylation / defense response to virus / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / negative regulation of translation / 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 / cytoplasm / cytosol
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 / Nucleic acid-binding proteins / S1 domain / 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
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: 2.8 Å
AuthorsDar, A.C. / Dever, T.E. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Higher-Order Substrate Recognition of eIF2alpha by the RNA-Dependent Protein Kinase PKR.
Authors: Dar, A.C. / Dever, T.E. / Sicheri, F.
History
DepositionJun 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3532
Polymers53,3532
Non-polymers00
Water27015
1
A: Eukaryotic translation initiation factor 2 alpha subunit
B: Interferon-induced, double-stranded RNA-activated protein kinase

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


Theoretical massNumber of molelcules
Total (without water)106,7074
Polymers106,7074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_794x-y+2,-y+4,-z-2/31
Unit cell
Length a, b, c (Å)84.300, 84.300, 165.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 20553.781 Da / Num. of mol.: 1 / Mutation: residue 258-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUI2, TIF211 / Plasmid: modified pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P20459
#2: Protein Interferon-induced, double-stranded RNA-activated protein kinase / Interferon-inducible RNA-dependent protein kinase / p68 kinase / P1/eIF-2A protein kinase


Mass: 32799.551 Da / Num. of mol.: 1 / Mutation: residue 3-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKR, EIF2AK2, PKR / Plasmid: modified pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS
References: UniProt: P19525, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.5 %
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 17397 / % possible obs: 99.5 % / Rsym value: 0.057 / Net I/σ(I): 24.3
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.454 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q46 for chain A and a PKR homology model (based on PDB entries 2CPK, 1BKX, 1FMO, 1ATP and 1BX6 for chain B.

1q46

2cpk

1bkx

1fmo

1atp

1bx6


Resolution: 2.8→29.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.651 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.206 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26837 1662 10 %RANDOM
Rwork0.2067 ---
obs0.21286 14967 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.17 Å20 Å2
2---0.35 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 0 15 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9754788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12924.39164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.21215702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21554
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22390
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.52200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98723454
X-RAY DIFFRACTIONr_scbond_it1.22831540
X-RAY DIFFRACTIONr_scangle_it2.0724.51334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 115 -
Rwork0.317 944 -
obs--87.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0190.08021.05183.38061.89395.65330.23060.0444-0.30380.0201-0.0830.10690.1991-0.2201-0.14750.03130.0269-0.05950.02870.0304-0.204743.68597.824-88.831
22.0919-1.3358-0.52843.46871.05032.159-0.0718-0.0965-0.16790.32120.2526-0.54190.43840.3095-0.18070.1666-0.0017-0.09570.1028-0.08-0.175449.843126.814-57.378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1753 - 175
2X-RAY DIFFRACTION1AC176 - 1831 - 8
3X-RAY DIFFRACTION2BB255 - 5411 - 274
4X-RAY DIFFRACTION2BD9 - 151 - 7

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