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- PDB-3uiu: Crystal structure of Apo-PKR kinase domain -

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Basic information

Entry
Database: PDB / ID: 3uiu
TitleCrystal structure of Apo-PKR kinase domain
ComponentsInterferon-induced, double-stranded RNA-activated protein kinase
KeywordsTRANSFERASE / kinase domain
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 / Resolution: 2.903 Å
AuthorsLi, F. / Li, S. / Yang, X. / Shen, Y. / Zhang, T.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Apo-PKR kinase domain
Authors: Li, F. / Li, S. / Yang, X. / Shen, Y. / Zhang, T.
History
DepositionNov 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,1372
Polymers71,1372
Non-polymers00
Water43224
1
A: Interferon-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)35,5681
Polymers35,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interferon-induced, double-stranded RNA-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)35,5681
Polymers35,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.412, 95.412, 122.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHRchain A and (resseq 254:336 or resseq 355:439 or resseq...AA254 - 3361 - 83
12SERSERLEULEUchain A and (resseq 254:336 or resseq 355:439 or resseq...AA355 - 439102 - 186
13THRTHRILEILEchain A and (resseq 254:336 or resseq 355:439 or resseq...AA451 - 460198 - 207
14TYRTYRLYSLYSchain A and (resseq 254:336 or resseq 355:439 or resseq...AA465 - 541212 - 288
21GLUGLUTHRTHRchain B and (resseq 254:336 or resseq 355:439 or resseq...BB254 - 3361 - 83
22SERSERLEULEUchain B and (resseq 254:336 or resseq 355:439 or resseq...BB355 - 439102 - 186
23THRTHRILEILEchain B and (resseq 254:336 or resseq 355:439 or resseq...BB451 - 460198 - 207
24TYRTYRLYSLYSchain B and (resseq 254:336 or resseq 355:439 or resseq...BB465 - 541212 - 288

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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 / PKR / Tyrosine-protein kinase EIF2AK2 / p68 kinase


Mass: 35568.488 Da / Num. of mol.: 2 / Fragment: PROTEIN KINASE DOMAIN, UNP RESIDUES 254-551
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE WAS BASED ON REF 18 OF DATABASE UNIPROTKB/SWISS-PROT P19525 (E2AK2_HUMAN).

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2M NaF, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14198 / % possible obs: 84.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 87.82 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.068
Reflection shellResolution: 2.9→3 Å / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.903→27.8 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6849 / SU ML: 0.44 / σ(F): 2 / Phase error: 36.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3048 1370 10.05 %RANDOM
Rwork0.2398 ---
all0.2467 14249 --
obs0.2467 13633 95.68 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.194 Å2 / ksol: 0.254 e/Å3
Displacement parametersBiso max: 161.82 Å2 / Biso mean: 98.0009 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.903→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 0 24 4102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114140
X-RAY DIFFRACTIONf_angle_d1.4025558
X-RAY DIFFRACTIONf_dihedral_angle_d17.8181548
X-RAY DIFFRACTIONf_chiral_restr0.091624
X-RAY DIFFRACTIONf_plane_restr0.005698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2036X-RAY DIFFRACTIONPOSITIONAL0.009
12B2036X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9034-3.00710.5561140.41541037115182
3.0071-3.12730.42611340.34191127126190
3.1273-3.26940.38591340.29131220135496
3.2694-3.44150.33241370.27561257139498
3.4415-3.65670.37891380.27351246138498
3.6567-3.93830.34371370.251257139499
3.9383-4.33330.33281410.20811269141099
4.3333-4.95730.24611440.20111258140299
4.9573-6.2340.33141370.23941297143499
6.234-27.80140.23791540.22081295144998

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