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- PDB-1qu6: STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1qu6
TitleSTRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION
ComponentsPROTEIN KINASE PKR
KeywordsTRANSFERASE / DSRNA-BINDING DOMAIN / PKR / SOLUTION STRUCTURE / PROTEIN KINASE
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / positive regulation of stress-activated MAPK cascade / regulation of hematopoietic progenitor cell differentiation / negative regulation of osteoblast proliferation / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / positive regulation of stress-activated MAPK cascade / regulation of hematopoietic progenitor cell differentiation / negative regulation of osteoblast proliferation / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / antiviral innate immune response / endoplasmic reticulum unfolded protein response / positive regulation of chemokine production / cellular response to amino acid starvation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / response to virus / non-membrane spanning protein tyrosine kinase activity / PKR-mediated signaling / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / Interferon alpha/beta signaling / double-stranded RNA binding / positive regulation of NF-kappaB transcription factor activity / kinase activity / defense response to virus / negative regulation of translation / positive regulation of MAPK cascade / protein autophosphorylation / 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 / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 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 / Alpha Beta
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / MODIFIED DG, SA PROTOCOL IN XPLOR
Model type detailsminimized average
AuthorsNanduri, S. / Carpick, B.W. / Yang, Y. / Williams, B.R.G. / Qin, J.
CitationJournal: EMBO J. / Year: 1998
Title: Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation.
Authors: Nanduri, S. / Carpick, B.W. / Yang, Y. / Williams, B.R. / Qin, J.
History
DepositionJul 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE PKR


Theoretical massNumber of molelcules
Total (without water)19,7051
Polymers19,7051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 90
RepresentativeModel #21minimized average structure

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Components

#1: Protein PROTEIN KINASE PKR


Mass: 19705.418 Da / Num. of mol.: 1 / Fragment: DSRNA-BINDING N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P19525, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D H(CCO)NH
1413D H(CCO)NH
1513D (H)CCH-TOCSY
1614D 15N
17113C EDITED NOESY
1814D 13C
1912D 15N HOHAHA
11013D 15N
11113D HNHA
11213D HNHB
11312D-ARO-(HB)CB(CGCD)HD
11412D-ARO (HB)CB(CGCDCE)HE

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA5001
Varian UNITY INOVAVarianUNITY INOVA6002

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGER, A. T.refinement
NMRPipestructure solution
PIPPstructure solution
RefinementMethod: MODIFIED DG, SA PROTOCOL IN XPLOR / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers calculated total number: 90 / Conformers submitted total number: 21

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