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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS
 
Authors :  J. Hu, J. Liu, R. Ghirlando, A. R. Saltiel, S. R. Hubbard
Date :  03 Dec 03  (Deposition) - 23 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Adapter Protein, Sh2 Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Hu, J. Liu, R. Ghirlando, A. R. Saltiel, S. R. Hubbard
Structural Basis For Recruitment Of The Adaptor Protein Aps To The Activated Insulin Receptor.
Mol. Cell V. 12 1379 2003
PubMed-ID: 14690593  |  Reference-DOI: 10.1016/S1097-2765(03)00487-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADAPTOR PROTEIN APS
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSH2 DOMAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:416 , ARG B:437 , SER B:439 , GLU B:440 , THR B:441BINDING SITE FOR RESIDUE SO4 B 101
2AC2SOFTWAREHOH A:22 , ARG A:416 , ARG A:437 , SER A:439 , GLU A:440 , THR A:441BINDING SITE FOR RESIDUE SO4 A 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B2_RAT409-507
 
  2A:409-488
B:409-493
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B2_RAT409-507
 
  2A:409-488
B:409-493
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SH2B2_RAT409-507
 
  4A:409-488
B:409-493

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000019351ENSRNOE00000319944chr12:21544434-21544670237SH2B2_RAT-00--
1.2ENSRNOT000000019352ENSRNOE00000013532chr12:21557200-21557933734SH2B2_RAT1-2362360--
1.3ENSRNOT000000019353ENSRNOE00000013533chr12:21562832-21562933102SH2B2_RAT237-270340--
1.4ENSRNOT000000019354ENSRNOE00000013534chr12:21564742-2156483392SH2B2_RAT271-301310--
1.5ENSRNOT000000019355ENSRNOE00000013542chr12:21565636-2156572792SH2B2_RAT301-332320--
1.6ENSRNOT000000019356ENSRNOE00000013543chr12:21565816-21565983168SH2B2_RAT332-388570--
1.7ENSRNOT000000019357ENSRNOE00000013544chr12:21567528-21567742215SH2B2_RAT388-459722A:403-459
B:404-459
57
56
1.8ENSRNOT000000019358ENSRNOE00000013538chr12:21570422-21570593172SH2B2_RAT460-517582A:460-488 (gaps)
B:460-493 (gaps)
29
34
1.9ENSRNOT000000019359ENSRNOE00000013539chr12:21571232-215722311000SH2B2_RAT517-6231070--

(-) 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:82
 aligned with SH2B2_RAT | Q9Z200 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:86
                                   412       422       432       442       452       462       472       482      
            SH2B2_RAT   403 ELSDYPWFHGTLSRVKAAQLVLAGGPRSHGLFVIRQSETRPGECVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVFDMLRHFHT 488
               SCOP domains d1rpya_ A: Adaptor protein Aps                                                         SCOP domains
               CATH domains 1rpyA00 A:403-488 SHC Adaptor Protein                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.......hhhhhhhhhhhhhhhhh..eeeee.......eeeeeee..eeeeee.----..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SH2  PDB: A:409-488 UniProt: 409-507                                             PROSITE
               Transcript 1 Exon 1.7  PDB: A:403-459 UniProt: 388-459 [INCOMPLETE]   Exon 1.8 UniProt: 460-517     Transcript 1
                 1rpy A 403 ELSDYPWFHGTLSRVKAAQLVLAGGPRSHGLFVIRQSETRPGECVLTFNFQGKAKHLRL----HGQCHVQHLWFQSVFDmLRHFHT 488
                                   412       422       432       442       452        |-   |   472       482      
                                                                                    461  466             482-MSE  

Chain B from PDB  Type:PROTEIN  Length:86
 aligned with SH2B2_RAT | Q9Z200 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:90
                                   413       423       433       443       453       463       473       483       493
            SH2B2_RAT   404 LSDYPWFHGTLSRVKAAQLVLAGGPRSHGLFVIRQSETRPGECVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVFDMLRHFHTHPIPL 493
               SCOP domains d1rpyb_ B: Adaptor protein Aps                                                             SCOP domains
               CATH domains 1rpyB00 B:404-493 SHC Adaptor Protein                                                      CATH domains
           Pfam domains (1) -----SH2-1rpyB01 B:409-486                                                         ------- Pfam domains (1)
           Pfam domains (2) -----SH2-1rpyB02 B:409-486                                                         ------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh..eeeee.......eeeeeee..eeeeeee.----.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----SH2  PDB: B:409-493 UniProt: 409-507                                                  PROSITE
               Transcript 1 Exon 1.7  PDB: B:404-459 UniProt: 388-459 [INCOMPLETE]  Exon 1.8  PDB: B:460-493 (gaps)    Transcript 1
                 1rpy B 404 LSDYPWFHGTLSRVKAAQLVLAGGPRSHGLFVIRQSETRPGECVLTFNFQGKAKHLRLS----GQCHVQHLWFQSVFDmLRHFHTHPIPL 493
                                   413       423       433       443       453        |-   |   473       483       493
                                                                                    462  467            482-MSE       

   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: SH2 (119)
1aSH2-1rpyB01B:409-486
1bSH2-1rpyB02B:409-486

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SH2B2_RAT | Q9Z200)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0035591    signaling adaptor activity    The binding activity of a molecule that brings together two or more molecules in a signaling pathway, permitting those molecules to function in a coordinated way. Adaptor molecules themselves do not have catalytic activity.
    GO:0005068    transmembrane receptor protein tyrosine kinase adaptor activity    The binding activity of a molecule that brings together a transmembrane receptor protein tyrosine kinase and one or more other molecules, permitting them to function in a coordinated way.
biological process
    GO:0001922    B-1 B cell homeostasis    The process of regulating the proliferation and elimination of B cells of the B-1 subset such that the total number of B-1 B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity.
    GO:0030036    actin cytoskeleton 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 and their associated proteins.
    GO:0050851    antigen receptor-mediated signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B or T cell.
    GO:0050873    brown fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0046578    regulation of Ras protein signal transduction    Any process that modulates the frequency, rate or extent of Ras protein signal transduction.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0019222    regulation of metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
    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.
cellular component
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

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 Related Entries

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        SH2B2_RAT | Q9Z2001rqq 1yvh

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