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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL SH2 DOMAIN OF MOUSE PHOSPHOLIPASE C-GAMMA 2
 
Authors :  N. Handa, T. Takagi, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Aug 06  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Phosphoric Diester Hydrolase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Takagi, N. Handa, K. Murayama, M. Shirouzu, T. Kurosaki, T. Terada, S. Yokoyama
Crystal Structure Of The N-Terminal Sh2 Domain Of Mouse Phospholipase C-Gamma 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE C, GAMMA 2
    ChainsA, B
    EngineeredYES
    Expression SystemCELL-FREE PROTEIN SYNTHESIS
    Expression System PlasmidPX060201-15
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL SH2 DOMAIN, RESIDUES 516-640
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A (1x)B (1x)
Biological Unit 3 (2x)A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:540 , ARG A:564 , SER A:566 , GLU A:567 , THR A:568 , THR A:574 , ARG B:582BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREHOH A:41 , HOH A:42 , HOH A:43 , LYS A:531 , TRP A:532 , ARG A:618 , ASN B:608 , SER B:609 , ALA B:612 , PRO B:634BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREHOH A:64 , ARG A:582 , ASN A:608 , SER B:566 , GLU B:567 , THR B:574 , ARG B:587BINDING SITE FOR RESIDUE SO4 B 1003

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:586 -A:624
2B:586 -B:624

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DX0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DX0)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.PLCG2_MOUSE532-635
646-735
  1A:532-635
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.PLCG2_MOUSE532-635
646-735
  1A:532-635
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.PLCG2_MOUSE532-635
646-735
  1A:532-635
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.PLCG2_MOUSE532-635
646-735
  2A:532-635
-

(-) Exons   (0, 0)

(no "Exon" information available for 2DX0)

(-) 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:117
 aligned with PLCG2_MOUSE | Q8CIH5 from UniProtKB/Swiss-Prot  Length:1265

    Alignment length:117
                                   529       539       549       559       569       579       589       599       609       619       629       
          PLCG2_MOUSE   520 DTPPTELHFGEKWFHKKVESRTSAEKLLQEYCAETGAKDGTFLVRESETFPNDYTLSFWRSGRVQHCRIRSTMENGVMKYYLTDNLTFNSIYALIQHYREAHLRCAEFELRLTDPVP 636
               SCOP domains d2dx0a_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh............hhhhhhhhhhhhhh........eeeee.......eeeeeee..eeeeeeeeeeee..eeeee........hhhhhhhhh......hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------SH2  PDB: A:532-635 UniProt: 532-635                                                                    - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2dx0 A 520 DTPPTELHFGEKWFHKKVESRTSAEKLLQEYCAETGAKDGTFLVRESETFPNDYTLSFWRSGRVQHCRIRSTMENGVMKYYLTDNLTFNSIYALIQHYREAHLRCAEFELRLTDPVP 636
                                   529       539       549       559       569       579       589       599       609       619       629       

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with PLCG2_MOUSE | Q8CIH5 from UniProtKB/Swiss-Prot  Length:1265

    Alignment length:97
                                   551       561       571       581       591       601       611       621       631       
          PLCG2_MOUSE   542 SAEKLLQEYCAETGAKDGTFLVRESETFPNDYTLSFWRSGRVQHCRIRSTMENGVMKYYLTDNLTFNSIYALIQHYREAHLRCAEFELRLTDPVPNP 638
               SCOP domains d2dx0b_ B: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.......eeeee....--.eeeeeee..eeeeeeeeeeee..eeeee.....ee.hhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SH2  PDB: - UniProt: 532-635                                                                  --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 2dx0 B 542 SAEKLLQEYCAETGAKDGTFLVRESETF--DYTLSFWRSGRVQHCRIRSTMENGVMKYYLTDNLTFNSIYALIQHYREAHLRCAEFELRLTDPVPNP 638
                                   551       561       | -|      581       591       601       611       621       631       
                                                     569  |                                                                  
                                                        572                                                                  

   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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DX0)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PLCG2_MOUSE | Q8CIH5)
molecular function
    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:0004435    phosphatidylinositol phospholipase C activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1,2-diacylglycerol + 1D-myo-inositol 1,4,5-trisphosphate + H(+).
    GO:0004629    phospholipase C activity    Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0032237    activation of store-operated calcium channel activity    A process that initiates the activity of an inactive store-operated calcium channel.
    GO:0002316    follicular B cell differentiation    The process in which a B cell in the spleen acquires the specialized features of a follicular B cell. Follicular B cells are major population of mature recirculating B cells in the spleen and are located in the B-cell follicle region.
    GO:0032959    inositol trisphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of inositol trisphosphate, 1,2,3,4,5,6-cyclohexanehexol, with three phosphate groups attached.
    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:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0043069    negative regulation of programmed cell death    Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    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:0009395    phospholipid catabolic process    The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0051209    release of sequestered calcium ion into cytosol    The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment.
    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:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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