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(-) Description

Authors :  L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Berg, E. Wahlberg, J. Weigelt, P. Nordlund, Structural Genomics Co (Sgc)
Date :  30 Jun 10  (Deposition) - 25 Aug 10  (Release) - 28 May 14  (Revision)
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Structural Genomics Consortium, Sgc, Phosphatidylinositol-3, 4, 5- Trisphosphate 5-Phosphatase 2, Ship2, Inppl1, Ship-2, Phosphatidylinositol, Phosphatase, Signalling, Magnesium, Structural Genomics Consortium Stockholm, Magnesium Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  L. Tresaugues, C. Silvander, S. Flodin, M. Welin, T. Nyman, S. Graslund, M. Hammarstrom, H. Berglund, P. Nordlund
Structural Basis For Phosphoinositide Substrate Recognition Catalysis, And Membrane Interactions In Human Inositol Polyphosphate 5-Phosphatases
Structure V. 22 744 2014
PubMed-ID: 24704254  |  Reference-DOI: 10.1016/J.STR.2014.01.013

(-) Compounds

    ChainsB, A
    EC Number3.1.3.1
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-MBP
    Expression System StrainBL21(DE3) R3 PRARE
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneINPPL1, SHIP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric Unit AB
Biological Unit 1 (1x) B
Biological Unit 2 (1x)A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NR8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
1Tyr B:661 -Arg B:662
2Tyr A:661 -Arg A:662

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric Unit (5, 10)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
2UniProtVAR_069587P659SSHIP2_HUMANDisease (OPSMD)397514510A/BP659S
3UniProtVAR_069588W688CSHIP2_HUMANDisease (OPSMD)  ---A/BW688C
5UniProtVAR_069589F722ISHIP2_HUMANDisease (OPSMD)397514512A/BF722I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
2UniProtVAR_069587P659SSHIP2_HUMANDisease (OPSMD)397514510BP659S
3UniProtVAR_069588W688CSHIP2_HUMANDisease (OPSMD)  ---BW688C
5UniProtVAR_069589F722ISHIP2_HUMANDisease (OPSMD)397514512BF722I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
2UniProtVAR_069587P659SSHIP2_HUMANDisease (OPSMD)397514510AP659S
3UniProtVAR_069588W688CSHIP2_HUMANDisease (OPSMD)  ---AW688C
5UniProtVAR_069589F722ISHIP2_HUMANDisease (OPSMD)397514512AF722I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NR8)

(-) Exons   (0, 0)

(no "Exon" information available for 3NR8)

(-) Sequences/Alignments

Asymmetric 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:293
 aligned with SHIP2_HUMAN | O15357 from UniProtKB/Swiss-Prot  Length:1258

    Alignment length:310
                                   431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..........hhhhhh...eee............eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeee.hhhhh.eeeeeeeee..--------..eeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhh........--hhhhh..eeeeeee.......hhhhhhhhhhh..hhhhhh.hhhhhhhhh................................-------.......eeeeee......eeeeeeee...........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I--------------------------S----------------------------C--------------------------------MI--------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                   431       441       451       461       471       481       491       501       511       521       531|      541       551       561       571       581       591  |    601       611       621       631       641       651       661       671   |     - |     691       701       711       721       731
                                                                                                                                        532      541                                               591  |                                                                              675     683                                                

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with SHIP2_HUMAN | O15357 from UniProtKB/Swiss-Prot  Length:1258

    Alignment length:312
                                   429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------Exo_endo_phos-3nr8B01 B:429-   718                                                                                                                                                                                                                                                                ------------- Pfam domains (1)
           Pfam domains (2) ---------Exo_endo_phos-3nr8B02 B:429-   718                                                                                                                                                                                                                                                                ------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee..........hhhhhh...eee...---......eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeee.hhhhh.eeeeeeeeee.------...eeeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhh..----...........eeeeeee.......hhhhhhhhhhh..hhhhhh.hhhhhhhhh..............................................eeeeee......eeeeeeee...........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I--------------------------S----------------------------C--------------------------------MI--------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                                   429       439       449      |  -|      469       479       489       499       509       519       529  |    539       549       559       569       579     |   -|      599       609       619       629       639       649       659       669       679       689       699       709       719       729  
                                                              456 460                                                                     532    539                                           585  590                                                                                                                                             

   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 3NR8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NR8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SHIP2_HUMAN | O15357)
molecular function
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0052659    inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0034485    phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity    Catalysis of the reaction: phosphatidylinositol-3,4,5-trisphosphate + H2O = phosphatidylinositol-3,4-bisphosphate + phosphate.
    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).
biological process
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0032868    response to insulin    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 insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0097178    ruffle assembly    The aggregation, arrangement and bonding together of a set of components to form a ruffle, a projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork. The formation of ruffles (also called membrane ruffling) is thought to be controlled by a group of enzymes known as Rho GTPases, specifically RhoA, Rac1 and cdc42.
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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        SHIP2_HUMAN | O153572k4p 2kso 2mk2 4a9c

(-) Related Entries Specified in the PDB File

3mtc 3n9v