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(-) Description

Title :  THE STRUCTURE OF SPLA-RYANODINE RECEPTOR DOMAIN AND SOCS BOX CONTAINING 1 IN COMPLEX WITH A PAR-4 PEPTIDE
 
Authors :  P. Filippakopoulos, A. Bullock, T. Keates, P. Savitsky, J. W. Murray, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, M. Wickstroem, C. Bount S. Knapp
Date :  22 Aug 08  (Deposition) - 16 Sep 08  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apoptosis, Transcription Regulation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Filippakopoulos, A. Low, T. D. Sharpe, J. Uppenberg, S. Yao, Z. Kuang, P. Savitsky, R. S. Lewis, S. E. Nicholson, R. S. Norton, A. Bullock
Structural Basis For Par-4 Recognition By The Spry Domain- And Socs Box-Containing Proteins Spsb1, Spsb2, And Spsb4.
J. Mol. Biol. V. 401 389 2010
PubMed-ID: 20561531  |  Reference-DOI: 10.1016/J.JMB.2010.06.017

(-) Compounds

Molecule 1 - SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 24-233
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPLA-RYANODINE RECEPTOR DOMAIN AND SOCS BOX CONTAINING 1
 
Molecule 2 - PRKC APOPTOSIS WT1 REGULATOR PROTEIN
    Chains: B
    Fragment: RESIDUES 67-81
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROSTATE APOPTOSIS RESPONSE 4 PROTEIN, PAR-4 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2JK9)

(-) Sites  (0, 0)

(no "Site" information available for 2JK9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JK9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JK9)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B302_SPRYPS50188 B30.2/SPRY domain profile.SPSB1_HUMAN33-231  1A:33-231
2SOCSPS50225 SOCS box domain profile.SPSB1_HUMAN221-273  1A:221-231

(-) Exons   (0, 0)

(no "Exon" information available for 2JK9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:202
 aligned with SPSB1_HUMAN | Q96BD6 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:202
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
          SPSB1_HUMAN    30 DYCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLD 231
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------SPRY-2jk9A01 A:95-229                                                                                                                  -- Pfam domains
         Sec.struct. author .....hhhhhhhhh...hhhhhhhh.eeeeee...eeee..eeeeeee.....eeeeeee.......eeeeeee.hhhhh....eeeee......eee...........eeeee....eeee.......ee...............eeeeeee....eeeeee..eeeeeee........eeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---B302_SPRY  PDB: A:33-231 UniProt: 33-231                                                                                                                                                                PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOCS        PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jk9 A  30 DYCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLD 231
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  


Chain B from PDB  Type:PROTEIN  Length:8
 aligned with PAWR_HUMAN | Q96IZ0 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:8
           PAWR_HUMAN    67 NELNNNLP  74
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2jk9 B   1 NELNNNLP   8
   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  (0, 0)

(no "SCOP Domain" information available for 2JK9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JK9)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SPRY] (6)

(-) Gene Ontology  (52, 54)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SPSB1_HUMAN | Q96BD6)
molecular function
    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:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
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.

Chain B   (PAWR_HUMAN | Q96IZ0)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0043522    leucine zipper domain binding    Interacting selectively and non-covalently with a leucine zipper domain, a protein secondary structure exhibiting a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns.
    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:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:0097202    activation of cysteine-type endopeptidase activity    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0071392    cellular response to estradiol stimulus    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0071372    cellular response to follicle-stimulating hormone stimulus    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 a follicle-stimulating hormone stimulus.
    GO:0071347    cellular response to interleukin-1    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 an interleukin-1 stimulus.
    GO:0071306    cellular response to vitamin E    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 a vitamin E stimulus.
    GO:0050966    detection of mechanical stimulus involved in sensory perception of pain    The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal.
    GO:0050965    detection of temperature stimulus involved in sensory perception of pain    The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal.
    GO:0042094    interleukin-2 biosynthetic process    The chemical reactions and pathways resulting in the formation of interleukin-2.
    GO:0030889    negative regulation of B cell proliferation    Any process that stops, prevents or reduces the rate or extent of B cell proliferation.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0090281    negative regulation of calcium ion import    Any process that decreases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045760    positive regulation of action potential    Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0042986    positive regulation of amyloid precursor protein biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta.
    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:0060450    positive regulation of hindgut contraction    Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine.
    GO:1903238    positive regulation of leukocyte tethering or rolling    Any process that activates or increases the frequency, rate or extent of leukocyte tethering or rolling.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:1904457    positive regulation of neuronal action potential    Any process that activates or increases the frequency, rate or extent of neuronal action potential.
    GO:2000391    positive regulation of neutrophil extravasation    Any process that activates or increases the frequency, rate or extent of neutrophil extravasation.
    GO:0032516    positive regulation of phosphoprotein phosphatase activity    Any process that activates or increases the activity of a phosphoprotein phosphatase.
    GO:1901082    positive regulation of relaxation of smooth muscle    Any process that activates or increases the frequency, rate or extent of relaxation of smooth muscle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0010040    response to iron(II) ion    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 iron(II) ion stimulus.
    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:0009611    response to wounding    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 indicating damage to the organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        SPSB1_HUMAN | Q96BD6: 3f2o

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