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(-) Description

Title :  PREDICTED STRUCTURE OF ALPHA-NEUROTOXIN HOMOLOG 1 FROM MICRURUS CORALLINUS, AND ITS BOUND ACETYLCHOLINE RECEPTOR PEPTIDE BY HOMOLOGY MODELING
 
Authors :  A. Bano, A. Salim, A. Abbasi, Z. H. Zaidi
Date :  23 Dec 04  (Deposition) - 11 Jan 05  (Release) - 11 Jan 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B
Keywords :  Alpha Neurotoxin Homolog, Homology Model, Comparative Modeling, Acetyl Choline Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Bano, A. Salim, A. Abbasi, Z. H. Zaidi
Prediction Of The Binding Sites In Alpha Neurotoxins From Some Elapidea Snakes: A Molecular Modeling Analysis Of The Subsequent Effect Of Binding On The Structure Of Neurotoxins
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-NEUROTOXIN HOMOLOG 1
    ChainsA
    Organism CommonBRAZILIAN CORAL SNAKE
    Organism ScientificMICRURUS CORALLINUS
 
Molecule 2 - 6 MER PEPTIDE FROM ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
    ChainsB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YCX)

(-) Sites  (0, 0)

(no "Site" information available for 1YCX)

(-) SS Bonds  (4, 4)

Theoretical Model
No.Residues
1A:3 -A:21
2A:16 -A:36
3A:38 -A:49
4A:50 -A:55

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SOC1_MICCO56-74  1A:35-53

(-) Exons   (1, 1)

Theoretical Model (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002610071bENSE00001914651chr2:175629189-175629080110ACHA_HUMAN1-15150--
1.2ENST000002610072ENSE00001016397chr2:175624361-175624216146ACHA_HUMAN15-63490--
1.3ENST000002610073ENSE00001693622chr2:175624103-17562405945ACHA_HUMAN64-78150--
1.4ENST000002610074ENSE00000882881chr2:175622748-17562267475ACHA_HUMAN79-103250--
1.5ENST000002610075ENSE00002067241chr2:175622403-175622294110ACHA_HUMAN104-140370--
1.6aENST000002610076aENSE00001635206chr2:175619142-175618947196ACHA_HUMAN140-205660--
1.7aENST000002610077aENSE00001755940chr2:175618468-175618231238ACHA_HUMAN206-285801B:229-2346
1.8ENST000002610078ENSE00001704617chr2:175614897-175614674224ACHA_HUMAN285-359750--
1.9ENST000002610079ENSE00001788243chr2:175613547-175613308240ACHA_HUMAN360-439800--
1.10bENST0000026100710bENSE00001840138chr2:175612983-175612388596ACHA_HUMAN440-482430--

(-) Sequences/Alignments

Theoretical Model
   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:57
 aligned with 3SOC1_MICCO | Q9PUB7 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:57
                                    31        41        51        61        71       
          3SOC1_MICCO    22 IVCYKRHASDSQTTTCLSGICYKKITRGISRPEMGCGCPQSSRGVKVECCMRDKCNG  78
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eee.....eeeee.......eeee.........eeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SNAKE_TOXIN        ---- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 1ycx A   1 IVCYKRHASDSQTTTCLSGICYKKITRGISRPEMGCGCPQSSRGVKVECCMRDKCNG  57
                                    10        20        30        40        50       

Chain B from PDB  Type:PROTEIN  Length:6
 aligned with ACHA_HUMAN | P02708 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:6
           ACHA_HUMAN   230 KHSVTY 235
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
               Transcript 1 1.7a   Transcript 1
                 1ycx B 229 KHSVTY 234

   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 1YCX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YCX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YCX)

(-) Gene Ontology  (33, 33)

Theoretical Model(hide GO term definitions)
Chain A   (3SOC1_MICCO | Q9PUB7)
cellular component
    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.

Chain B   (ACHA_HUMAN | P02708)
molecular function
    GO:0042166    acetylcholine binding    Interacting selectively and non-covalently with acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.
    GO:0015464    acetylcholine receptor activity    Combining with acetylcholine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0005230    extracellular ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0015276    ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
biological process
    GO:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0099565    chemical synaptic transmission, postsynaptic    The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0046716    muscle cell cellular homeostasis    The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state.
    GO:0050881    musculoskeletal movement    The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system.
    GO:0007528    neuromuscular junction development    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
    GO:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0007274    neuromuscular synaptic transmission    The process of synaptic transmission from a neuron to a muscle, across a synapse.
    GO:0070050    neuron cellular homeostasis    The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state.
    GO:0019228    neuronal action potential    An action potential that occurs in a neuron.
    GO:0042391    regulation of membrane potential    Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0035094    response to nicotine    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 nicotine stimulus.
    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:0003009    skeletal muscle contraction    A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
    GO:0048630    skeletal muscle tissue growth    The increase in size or mass of a skeletal muscle. This may be due to a change in the fiber number or size.
    GO:0007271    synaptic transmission, cholinergic    The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005892    acetylcholine-gated channel complex    A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    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:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    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
        3SOC1_MICCO | Q9PUB71ycv
        ACHA_HUMAN | P027081y5p 1y5t 1y6c 4zjs

(-) Related Entries Specified in the PDB File

1ycv ALPHA-NEUROTOXIN HOMOLOG 1