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(-) Description

Title :  MODULATION OF AGRIN FUNCTION BY ALTERNATIVE SPLICING AND CA2+ BINDING
 
Authors :  J. Stetefeld, A. T. Alexandrescu, M. W. Maciejewski, M. Jenny, K. Rathgeb-Szabo, T. Schulthess, R. Landwehr, S. Frank, M. A. Ruegg, R. A. Kammerer
Date :  10 Jul 03  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Agrin, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Stetefeld, A. T. Alexandrescu, M. W. Maciejewski, M. Jenny, K. Rathgeb-Szabo, T. Schulthess, R. Landwehr, S. Frank, M. A. Ruegg, R. A. Kammerer
Modulation Of Agrin Function By Alternative Splicing And Ca2+ Binding.
Structure V. 12 503 2004
PubMed-ID: 15016366  |  Reference-DOI: 10.1016/J.STR.2004.02.001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGRIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentBASAL LAMINA DOMAIN
    GeneAGRN
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/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
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:73 , LEU A:90 , GLN A:140 , ASP A:142BINDING SITE FOR RESIDUE CA A 701
2AC2SOFTWAREASP B:73 , LEU B:90 , GLN B:140 , ASP B:142BINDING SITE FOR RESIDUE CA B 702
3AC3SOFTWAREASP C:73 , LEU C:90 , GLN C:140 , ASP C:142BINDING SITE FOR RESIDUE CA C 703
4AC4SOFTWAREASP D:73 , LEU D:90 , GLN D:140 , ASP D:142 , HOH D:764BINDING SITE FOR RESIDUE CA D 704

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:172 -A:198
2B:172 -B:198
3C:172 -C:198
4D:172 -D:198

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PZ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PZ8)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.AGRIN_CHICK1388-1563
1650-1836
1902-2078
 
 
 
  4-
-
A:41-198
B:41-198
C:41-198
D:41-198
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.AGRIN_CHICK1388-1563
1650-1836
1902-2078
 
 
 
  1-
-
A:41-198
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.AGRIN_CHICK1388-1563
1650-1836
1902-2078
 
 
 
  1-
-
-
B:41-198
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.AGRIN_CHICK1388-1563
1650-1836
1902-2078
 
 
 
  1-
-
-
-
C:41-198
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.AGRIN_CHICK1388-1563
1650-1836
1902-2078
 
 
 
  1-
-
-
-
-
D:41-198

(-) Exons   (0, 0)

(no "Exon" information available for 1PZ8)

(-) 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:176
 aligned with AGRIN_CHICK | P31696 from UniProtKB/Swiss-Prot  Length:2081

    Alignment length:197
                                  1891      1901      1911      1921      1931      1941      1951      1961      1971      1981      1991      2001      2011      2021      2031      2041      2051      2061      2071       
         AGRIN_CHICK   1882 EAIAFDGRTYMEYHNAVTKSHLSNEIPAPDALDYPAEPSEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC 2078
               SCOP domains d1pz8a_ A: Agrin                                                                                                                                                                                      SCOP domains
               CATH domains 1pz8A00 A:13-198                       [code=2.60.120.200, no name defined]                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eeee...---------------------..eee.eeeeeeeeee....eeeeee........eeeeeee..eeeeeee.....eeeeeeee......eeeeeeee..eeeeee.....eeee.......eee..eeee............hhhhhh..eeeeeeeee..ee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------LAM_G_DOMAIN  PDB: A:41-198 UniProt: 1902-2078                                                                                                                                    PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pz8 A   13 EAIAFDGRTYMEYHNAV---------------------AEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC  198
                                    22      |  -         -        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
                                           29                    40                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with AGRIN_CHICK | P31696 from UniProtKB/Swiss-Prot  Length:2081

    Alignment length:199
                                  1889      1899      1909      1919      1929      1939      1949      1959      1969      1979      1989      1999      2009      2019      2029      2039      2049      2059      2069         
         AGRIN_CHICK   1880 DAEAIAFDGRTYMEYHNAVTKSHLSNEIPAPDALDYPAEPSEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC 2078
               SCOP domains d1pz8b_ B: Agrin                                                                                                                                                                                        SCOP domains
               CATH domains 1pz8B00 B:11-198  [c                    ode=2.60.120.200, no name defined]                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eee.....--------------------..eee.eeeeeeeeee....eeeeee........eeeeeee..eeeeeee.....eeeeeeee......eeeeeeee..eeeeee.....eeee.......eee...eee............hhhhhh..eeeeeeeee..ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------LAM_G_DOMAIN  PDB: B:41-198 UniProt: 1902-2078                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pz8 B   11 DAEAIAFDGRTYMEYHNAVT--------------------AEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC  198
                                    20        30         -         -|       49        59        69        79        89        99       109       119       129       139       149       159       169       179       189         
                                              30                   40                                                                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with AGRIN_CHICK | P31696 from UniProtKB/Swiss-Prot  Length:2081

    Alignment length:198
                                  1890      1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040      2050      2060      2070        
         AGRIN_CHICK   1881 AEAIAFDGRTYMEYHNAVTKSHLSNEIPAPDALDYPAEPSEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC 2078
               SCOP domains d1pz8c_ C: Agrin                                                                                                                                                                                       SCOP domains
               CATH domains 1pz8C00 C:12-198                        [code=2.60.120.200, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....eeee...----------------------.eee.eeeeeeeeee...eeeeeee........eeeeeee..eeeeeee.....eeeeeeee......eeeeeeee..eeeeee.....eeee.......eee..eeee............hhhhhh..eeeeeeeee..ee.............ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------LAM_G_DOMAIN  PDB: C:41-198 UniProt: 1902-2078                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1pz8 C   12 AEAIAFDGRTYMEYHNAV----------------------EKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC  198
                                    21       | -         -         -|       50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
                                            29                     41                                                                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:177
 aligned with AGRIN_CHICK | P31696 from UniProtKB/Swiss-Prot  Length:2081

    Alignment length:198
                                  1890      1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040      2050      2060      2070        
         AGRIN_CHICK   1881 AEAIAFDGRTYMEYHNAVTKSHLSNEIPAPDALDYPAEPSEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC 2078
               SCOP domains d1pz8d_ D: Agrin                                                                                                                                                                                       SCOP domains
               CATH domains 1pz8D00 D:12-198                       [code=2.60.120.200, no name defined]                                                                                                                            CATH domains
           Pfam domains (1) --------------------------------------------Laminin_G_1-1pz8D01 D:45-176                                                                                                        ---------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Laminin_G_1-1pz8D02 D:45-176                                                                                                        ---------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------Laminin_G_1-1pz8D03 D:45-176                                                                                                        ---------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------Laminin_G_1-1pz8D04 D:45-176                                                                                                        ---------------------- Pfam domains (4)
         Sec.struct. author ...eeee....eeee...---------------------..eee.eeeeeeeeee....eeeeee........eeeeeee..eeeeeee....eeeeeeeee......eeeeeeee..eeeeee.....eeee.......eee..eeee......hhhhhhhhhhhh..eeeeeeeee..ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------LAM_G_DOMAIN  PDB: D:41-198 UniProt: 1902-2078                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1pz8 D   12 AEAIAFDGRTYMEYHNAV---------------------AEKALQSNHFELSIKTEATQGLILWSGKGLERSDYIALAIVDGFVQMMYDLGSKPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSPLGATQLDTDGALWLGGMERLSVAHKLPKAYSTGFIGCIRDVIVDRQELHLVEDALNNPTILHC  198
                                    21       | -         -        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
                                            29                    40                                                                                                                                                              

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (AGRIN_CHICK | P31696)
molecular function
    GO:0030548    acetylcholine receptor regulator activity    Interacting (directly or indirectly) with acetylcholine receptors such that the proportion of receptors in the active form is changed.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0035374    chondroitin sulfate binding    Interacting selectively and non-covalently with chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc).
    GO:0002162    dystroglycan binding    Interacting selectively and non-covalently with dystroglycan. Dystroglycan is glycoprotein found in non-muscle tissues as well as in muscle tissues, often in association with dystrophin. The native dystroglycan cleaved into two non-covalently associated subunits, alpha (N-terminal) and beta (C-terminal).
    GO:0043395    heparan sulfate proteoglycan binding    Interacting selectively and non-covalently with a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0043236    laminin binding    Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0033691    sialic acid binding    Interacting selectively and non-covalently with sialic acid, any of a variety of N- or O- substituted derivatives of neuraminic acid, a nine carbon monosaccharide. Sialic acids often occur in polysaccharides, glycoproteins, and glycolipids in animals and bacteria.
    GO:0030297    transmembrane receptor protein tyrosine kinase activator activity    Binds to and increases the activity of a transmembrane receptor protein tyrosine kinase.
biological process
    GO:0007213    G-protein coupled acetylcholine receptor signaling pathway    Any series of molecular signals initiated by an acetylcholine receptor on the surface of the target cell binding to one of its physiological ligands, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction and ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0007171    activation of transmembrane receptor protein tyrosine kinase activity    Any process that initiates the activity of the inactive transmembrane receptor protein tyrosine kinase activity.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0051491    positive regulation of filopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0045887    positive regulation of synaptic growth at neuromuscular junction    Any process that activates or increases the frequency, rate or extent of synaptic growth at neuromuscular junction.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    GO:0099601    regulation of neurotransmitter receptor activity    Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity. Modulation may be via an effect on ligand affinity, or effector funtion such as ion selectivity or pore opening/closing in ionotropic receptors.
cellular component
    GO:0005605    basal lamina    A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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: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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AGRIN_CHICK | P316961jb3 1jc7 1pxu 1pz7 1pz9 1q56 3i70

(-) Related Entries Specified in the PDB File

1pz7 G3 DOMAIN OF AGRIN WITH B11 INSERT AND CALCIUM
1q56 NMR STRUCTURE OF THE B0 ISOFORM OF THE AGRIN G3 DOMAIN IN ITS CA2+ BOUND STATE