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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ABRIDGED FORM OF THE MATURE ECTODOMAIN OF THE HUMAN RECEPTOR-TYPE PROTEIN TYROSINE PHOSPHATASE ICA512/IA-2 AT PH 8.5
 
Authors :  M. E. Primo, J. Jakoncic, E. Poskus, M. R. Ermacora
Date :  13 May 10  (Deposition) - 24 Nov 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Ia-2, Ica-512, Protein-Tyrosine Phosphatase, Transmembrane Protein, Diabetes, Autoimmunity, Proteolysis, Glycoprotein, Receptor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Primo, J. Jakoncic, E. Poskus, M. R. Ermacora
Receptor-Type Protein-Tyrosine Phosphatase Ia-2-Ica512
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE-LIKE N
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET9B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 470-558
    GeneICA3, ICA512, PTPRN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymR-PTP-N, PTP IA-2, ISLET CELL ANTIGEN 512, ICA 512, ISLET CELL AUTOANTIGEN 3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:498 , HOH A:705 , GLU B:542 , GLN B:548 , HOH B:708 , HOH B:807BINDING SITE FOR RESIDUE CA B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N01)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:479 -Pro A:480
2Lys B:479 -Pro B:480

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N01)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002957181bENSE00001843122chr2:220174295-220173940356PTPRN_HUMAN1-39390--
1.4cENST000002957184cENSE00001609781chr2:220172564-22017251451PTPRN_HUMAN39-56180--
1.4fENST000002957184fENSE00001646399chr2:220172279-220172166114PTPRN_HUMAN56-94390--
1.6bENST000002957186bENSE00001689890chr2:220168553-22016845797PTPRN_HUMAN94-126330--
1.7eENST000002957187eENSE00001669026chr2:220167559-220167298262PTPRN_HUMAN126-213880--
1.8cENST000002957188cENSE00001779946chr2:220167213-220166859355PTPRN_HUMAN214-3321190--
1.9ENST000002957189ENSE00001803105chr2:220166441-220166310132PTPRN_HUMAN332-376450--
1.10ENST0000029571810ENSE00001680212chr2:220165699-22016566535PTPRN_HUMAN376-387120--
1.11ENST0000029571811ENSE00001790646chr2:220164981-220164707275PTPRN_HUMAN388-479922A:470-479
B:470-479
10
10
1.12ENST0000029571812ENSE00001792556chr2:220164508-22016442287PTPRN_HUMAN479-508302A:479-508
B:479-508
30
30
1.13cENST0000029571813cENSE00001663640chr2:220164106-22016402780PTPRN_HUMAN508-535282A:508-535
B:508-535 (gaps)
28
28
1.13dENST0000029571813dENSE00001722334chr2:220163833-22016376965PTPRN_HUMAN535-556222A:535-556
B:535-556
22
22
1.14bENST0000029571814bENSE00001641294chr2:220162825-220162607219PTPRN_HUMAN557-629730--
1.15bENST0000029571815bENSE00001804219chr2:220162155-220161955201PTPRN_HUMAN630-696670--
1.16ENST0000029571816ENSE00001596701chr2:220161854-220161707148PTPRN_HUMAN697-746500--
1.17aENST0000029571817aENSE00001787617chr2:220161544-22016147174PTPRN_HUMAN746-770250--
1.18ENST0000029571818ENSE00001642327chr2:220161238-22016116178PTPRN_HUMAN771-796260--
1.19aENST0000029571819aENSE00001671885chr2:220161067-220160948120PTPRN_HUMAN797-836400--
1.19dENST0000029571819dENSE00001770552chr2:220159863-220159697167PTPRN_HUMAN837-892560--
1.20bENST0000029571820bENSE00001650195chr2:220156245-22015619254PTPRN_HUMAN892-910190--
1.21ENST0000029571821ENSE00001687150chr2:220155612-22015554865PTPRN_HUMAN910-932230--
1.22ENST0000029571822ENSE00001766807chr2:220155333-22015526074PTPRN_HUMAN932-956250--
1.23eENST0000029571823eENSE00001775602chr2:220155019-220154345675PTPRN_HUMAN957-979230--

(-) 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:87
 aligned with PTPRN_HUMAN | Q16849 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:87
                                   479       489       499       509       519       529       539       549       
          PTPRN_HUMAN   470 EYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHNEQNLSLADVTQQAGLVKSELEAQTGLQILQTGVGQ 556
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeeee..eeeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11 ----------------------------Exon 1.13c  PDB: A:508-535  --------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.12  PDB: A:479-508     --------------------------Exon 1.13d             Transcript 1 (2)
                 3n01 A 470 EYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHNEQNLSLADVTQQAGLVKSELEAQTGLQILQTGVGQ 556
                                   479       489       499       509       519       529       539       549       

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with PTPRN_HUMAN | Q16849 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:87
                                   479       489       499       509       519       529       539       549       
          PTPRN_HUMAN   470 EYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHNEQNLSLADVTQQAGLVKSELEAQTGLQILQTGVGQ 556
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Receptor_IA-2-3n01B01 B:470-556                                                         Pfam domains (1)
           Pfam domains (2) Receptor_IA-2-3n01B02 B:470-556                                                         Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeeee..eeeeee...---.hhhhhhhhhhhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11 ----------------------------Exon 1.13c UniProt: 508-535 --------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.12  PDB: B:479-508     --------------------------Exon 1.13d             Transcript 1 (2)
                 3n01 B 470 EYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHN---LSLADVTQQAGLVKSELEAQTGLQILQTGVGQ 556
                                   479       489       499       509       519 |   | 529       539       549       
                                                                             521 525                               

   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 3N01)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N01)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PTPRN_HUMAN | Q16849)
molecular function
    GO:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
biological process
    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:1990502    dense core granule maturation    Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis.
    GO:0030073    insulin secretion    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
    GO:0035773    insulin secretion involved in cellular response to glucose stimulus    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin, in response to a glucose stimulus.
    GO:0001553    luteinization    The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation.
    GO:0051591    response to cAMP    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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0043627    response to estrogen    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 an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0009749    response to glucose    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 glucose stimulus.
    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:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
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: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:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    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.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTPRN_HUMAN | Q168492i1y 2qt7 3n4w 3ng8 3np5

(-) Related Entries Specified in the PDB File

2qt7 A LARGER VERSION OF THE MATURE ECTODOMAIN OF IA-2-ICA512