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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF HUMAN SIN1, A TORC2 SUBUNIT
 
Authors :  D. Pan, Y. Matsuura
Date :  31 Jan 12  (Deposition) - 11 Apr 12  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ph Domain, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Pan, Y. Matsuura
Structures Of The Pleckstrin Homology Domain Of Saccharomyces Cerevisiae Avo1 And Its Human Orthologue Sin1 An Essential Subunit Of Tor Complex 2
Acta Crystallogr. , Sect. F V. 68 386 2012
PubMed-ID: 22505404  |  Reference-DOI: 10.1107/S1744309112007178

(-) Compounds

Molecule 1 - TARGET OF RAPAMYCIN COMPLEX 2 SUBUNIT MAPKAP1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A-TEV
    Expression System StrainBL21-CODONPLUS(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL PH DOMAIN, UNP RESIDUES 372-493
    GeneSIN1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTORC2 SUBUNIT MAPKAP1, MITOGEN-ACTIVATED PROTEIN KINASE 2- ASSOCIATED PROTEIN 1, STRESS-ACTIVATED MAP KINASE-INTERACTING PROTEIN 1, SAPK-INTERACTING PROTEIN 1, MSIN1

 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 3VOQ)

(-) Sites  (0, 0)

(no "Site" information available for 3VOQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VOQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VOQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VOQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VOQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3VOQ)

(-) 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:116
 aligned with SIN1_HUMAN | Q9BPZ7 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:130
                                   370       380       390       400       410       420       430       440       450       460       470       480       490
           SIN1_HUMAN   361 GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKASTKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVLKVNYILESRA 490
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h--------hhhhhhhhhh....eeeeeeeee...eeeeeeeee...eeeeee.------.........eeee...eeeeeeeee.....eeeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3voq A 369 G--------AMATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPV------TKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVLKVNYILESRA 490
                            |      370       380       390       400       410   |     -|      430       440       450       460       470       480       490
                            |      370                                         414    421                                                                     
                          369                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with SIN1_HUMAN | Q9BPZ7 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:131
                                   370       380       390       400       410       420       430       440       450       460       470       480       490 
           SIN1_HUMAN   361 GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKASTKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVLKVNYILESRAS 491
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------hhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeee...eeeeee.----------.....eeee...eeeeeeeeeee..eeeeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3voq B 369 G--------AMATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPV----------IKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVLKVNYILESRAS 491
                            |      370       380       390       400       410   |     -    |  430       440       450       460       470       480       490 
                          369      370                                         414        425                                                                  

   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 3VOQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VOQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VOQ)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SIN1_HUMAN | Q9BPZ7)
molecular function
    GO:0017016    Ras GTPase binding    Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
    GO:0070300    phosphatidic acid binding    Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0005547    phosphatidylinositol-3,4,5-trisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    GO:0080025    phosphatidylinositol-3,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0046580    negative regulation of Ras protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0021762    substantia nigra development    The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0031932    TORC2 complex    A protein complex that contains at least TOR (target of rapamycin) and Rictor (rapamycin-insensitive companion of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of PKB (also called AKT). In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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 Specified in the PDB File

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