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(-) Description

Title :  STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION
 
Authors :  S. Nanduri, B. W. Carpick, Y. Yang, B. R. G. Williams, J. Qin
Date :  08 Jul 99  (Deposition) - 23 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Dsrna-Binding Domain, Nmr, Pkr, Solution Structure, Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Nanduri, B. W. Carpick, Y. Yang, B. R. Williams, J. Qin
Structure Of The Double-Stranded Rna-Binding Domain Of The Protein Kinase Pkr Reveals The Molecular Basis Of Its Dsrna-Mediated Activation.
Embo J. V. 17 5458 1998
PubMed-ID: 9736623  |  Reference-DOI: 10.1093/EMBOJ/17.18.5458
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN KINASE PKR
    ChainsA
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDSRNA-BINDING N-TERMINAL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (21x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QU6)

(-) Sites  (0, 0)

(no "Site" information available for 1QU6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QU6)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.E2AK2_HUMAN9-77
100-167
  2A:14-82
A:105-172

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003951271bENSE00001479941chr2:37384190-37384051140E2AK2_HUMAN-00--
1.2aENST000003951272aENSE00001520686chr2:37376400-37376000401E2AK2_HUMAN-00--
1.3aENST000003951273aENSE00000809607chr2:37374965-37374831135E2AK2_HUMAN1-40401A:6-4540
1.4aENST000003951274aENSE00000747498chr2:37374116-37373996121E2AK2_HUMAN40-80411A:45-8541
1.5cENST000003951275cENSE00000747497chr2:37368844-37368696149E2AK2_HUMAN81-130501A:86-13550
1.6ENST000003951276ENSE00000747496chr2:37366900-37366774127E2AK2_HUMAN130-172431A:135-17541
1.7ENST000003951277ENSE00000747494chr2:37365728-3736565277E2AK2_HUMAN173-198261A:176-179 (gaps)9
1.8ENST000003951278ENSE00000747492chr2:37365506-3736541394E2AK2_HUMAN198-229320--
1.9aENST000003951279aENSE00000747490chr2:37364160-3736412635E2AK2_HUMAN230-241120--
1.10ENST0000039512710ENSE00000747488chr2:37362689-3736262763E2AK2_HUMAN241-262220--
1.11ENST0000039512711ENSE00000747487chr2:37353554-37353432123E2AK2_HUMAN262-303420--
1.12ENST0000039512712ENSE00000747486chr2:37349807-37349649159E2AK2_HUMAN303-356540--
1.13bENST0000039512713bENSE00000397476chr2:37347282-37347102181E2AK2_HUMAN356-416610--
1.15ENST0000039512715ENSE00000747412chr2:37342002-37341874129E2AK2_HUMAN417-459430--
1.16bENST0000039512716bENSE00000747411chr2:37336438-37336337102E2AK2_HUMAN460-493340--
1.17ENST0000039512717ENSE00000747410chr2:37334670-3733461754E2AK2_HUMAN494-511180--
1.18cENST0000039512718cENSE00001520668chr2:37334538-37333699840E2AK2_HUMAN512-551400--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:179
 aligned with E2AK2_HUMAN | P19525 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:191
                                 1                                                                                                                                                                                         
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185 
          E2AK2_HUMAN     - -----MAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTVNYEQCASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQILSEETSVKSDYLSSGSFATTC 186
               SCOP domains d1qu6a1 A:1-90 dsRNA-dependent protein kinase pkr                                         d1qu6a2 A:91-179 dsRNA-dependent protein kinase pkr                                                   SCOP domains
               CATH domains 1qu6A01 A:1-85  [code=3.30.160.20, no name defined]                                  ------------------1qu6A02 A:104-179  [code=3.30.160.20, no name defined]                                   CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------dsrm-1qu6A01 A:106-170                                           --------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------dsrm-1qu6A02 A:106-170                                           --------------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhh...eeeeee.........eeeeee.......eee...hhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhh..eeeeeeeee......eeeeeeeee.....eeee.hhhhhhhhhhhhhhhhhhhh..-------...-----. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------DS_RBD  PDB: A:14-82 UniProt: 9-77                                   ----------------------DS_RBD  PDB: A:105-172 UniProt: 100-167                             ------------------- PROSITE
           Transcript 1 (1) -----Exon 1.3a  PDB: A:6-45 UniProt: 1-40    ----------------------------------------Exon 1.5c  PDB: A:86-135 UniProt: 81-130          ------------------------------------------Exon 1.7       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.4a  PDB: A:45-85 UniProt: 40-80   -------------------------------------------------Exon 1.6  PDB: A:135-175 UniProt: 130-172  -------------- Transcript 1 (2)
                 1qu6 A   1 GSHMEMAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTVNYEQCASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQILSEET-------GSG-----C 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    |    -  | |    -|
                                                                                                                                                                                                        175     176 |   179
                                                                                                                                                                                                                  178      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: DSRM (45)
(-)
Family: dsrm (27)
1adsrm-1qu6A01A:106-170
1bdsrm-1qu6A02A:106-170

(-) Gene Ontology  (58, 58)

NMR Structure(hide GO term definitions)
Chain A   (E2AK2_HUMAN | P19525)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004694    eukaryotic translation initiation factor 2alpha kinase activity    Catalysis of the reaction: ATP + [eukaryotic translation initiation factor 2 alpha subunit] = ADP + [eukaryotic translation initiation factor 2 alpha subunit] phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0034198    cellular response to amino acid starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of amino acids.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0033689    negative regulation of osteoblast proliferation    Any process that stops, prevents or reduces the rate or extent of osteoblast proliferation.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:1901224    positive regulation of NIK/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of NIK/NF-kappaB signaling.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0032722    positive regulation of chemokine production    Any process that activates or increases the frequency, rate, or extent of chemokine production.
    GO:0001819    positive regulation of cytokine production    Any process that activates or increases the frequency, rate or extent of production of a cytokine.
    GO:0032874    positive regulation of stress-activated MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:1900225    regulation of NLRP3 inflammasome complex assembly    Any process that modulates the frequency, rate or extent of NLRP3 inflammasome complex assembly.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:1901532    regulation of hematopoietic progenitor cell differentiation    Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation.
    GO:1902036    regulation of hematopoietic stem cell differentiation    Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.
    GO:1902033    regulation of hematopoietic stem cell proliferation    Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010998    regulation of translational initiation by eIF2 alpha phosphorylation    Any process that modulates the frequency, rate or extent of translation initiation in response to stress by the phosphorylation of eIF2 alpha.
    GO:0043330    response to exogenous dsRNA    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus.
    GO:0035455    response to interferon-alpha    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO:0033197    response to vitamin E    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin E stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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        E2AK2_HUMAN | P195252a19 2a1a 3uiu

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