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(-) Description

Title :  SOLUTION STRUCTURE OF THE HUMAN VOLTAGE-GATED SODIUM CHANNEL, BRAIN ISOFORM (NAV1.2)
 
Authors :  V. Z. Miloushev, J. A. Levine, M. A. Arbing, J. F. Hunt, G. S. Pitt, A. G. Pa
Date :  15 Nov 08  (Deposition) - 06 Jan 09  (Release) - 23 Jun 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Voltage-Gated Sodium Channel, Alternative Splicing, Disease Mutation, Epilepsy, Glycoprotein, Ion Transport, Ionic Channel, Membrane, Polymorphism, Sodium, Sodium Channel, Sodium Transport, Transmembrane, Transport, Ubl Conjugation, Voltage-Gated Channel, Transport Protein, Transport Protein Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Z. Miloushev, J. A. Levine, M. A. Arbing, J. F. Hunt, G. S. Pitt, A. G. Palmer
Solution Structure Of The Nav1. 2 C-Terminal Ef-Hand Domain.
J. Biol. Chem. V. 284 6446 2009
PubMed-ID: 19129176  |  Reference-DOI: 10.1074/JBC.M807401200

(-) Compounds

Molecule 1 - SODIUM CHANNEL PROTEIN TYPE 2 SUBUNIT ALPHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid562
    Expression System VectorPET28
    FragmentC-TERMINAL EF-HAND DOMAIN
    GeneNAC2, SCN2A, SCN2A1, SCN2A2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSODIUM CHANNEL PROTEIN TYPE II SUBUNIT ALPHA, VOLTAGE-GATED SODIUM CHANNEL SUBUNIT ALPHA NAV1.2, SODIUM CHANNEL PROTEIN, BRAIN II SUBUNIT ALPHA, HBSC II

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KAV)

(-) Sites  (0, 0)

(no "Site" information available for 2KAV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KAV)

(-) Cis Peptide Bonds  (2, 30)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Pro A:1827 -Pro A:1828
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Lys A:1833 -Pro A:1834

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_078484D1823ASCN2A_HUMANUnclassified138497939AD1823A
2UniProtVAR_078485R1882GSCN2A_HUMANDisease796053166AR1882G
3UniProtVAR_078486R1882LSCN2A_HUMANDisease (EIEE11)794727444AR1882L
4UniProtVAR_078201R1882QSCN2A_HUMANDisease (EIEE11)794727444AR1882Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KAV)

(-) Exons   (0, 0)

(no "Exon" information available for 2KAV)

(-) Sequences/Alignments

NMR Structure
   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:106
 aligned with SCN2A_HUMAN | Q99250 from UniProtKB/Swiss-Prot  Length:2005

    Alignment length:106
                                  1786      1796      1806      1816      1826      1836      1846      1856      1866      1876      
         SCN2A_HUMAN   1777 ENFSVATEESAEPLSEDDFEMFYEVWEKFDPDATQFIEFAKLSDFADALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDALRIQMEER 1882
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh..........hhhhhhh...ee...eeehhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------A----------------------------------------------------------G SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------L SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------------------Q SAPs(SNPs) (3)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                2kav A 1777 ENFSVATEESAEPLSEDDFEMFYEVWEKFDPDATQFIEFAKLSDFADALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDALRIQMEER 1882
                                  1786      1796      1806      1816      1826      1836      1846      1856      1866      1876      

   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 2KAV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (SCN2A_HUMAN | Q99250)
molecular function
    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:0005272    sodium channel activity    Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
    GO:0005248    voltage-gated sodium channel activity    Enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0008627    intrinsic apoptotic signaling pathway in response to osmotic stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to changes in intracellular ion homeostasis, and ends when the execution phase of apoptosis is triggered.
    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:0086010    membrane depolarization during action potential    The process in which membrane potential changes in the depolarizing direction from the negative resting potential towards the positive membrane potential that will be the peak of the action potential.
    GO:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    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:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0019228    neuronal action potential    An action potential that occurs in a neuron.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0060078    regulation of postsynaptic membrane potential    Any process that modulates the potential difference across a post-synaptic membrane.
    GO:0035725    sodium ion transmembrane transport    A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006814    sodium ion transport    The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0030315    T-tubule    Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
    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: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:0005887    integral component of plasma membrane    The component of the plasma 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:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0033268    node of Ranvier    An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed.
    GO:0033270    paranode region of axon    An axon part that is located adjacent to the nodes of Ranvier and surrounded by lateral loop portions of myelin sheath.
    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:0034706    sodium channel complex    An ion channel complex through which sodium ions pass.
    GO:0001518    voltage-gated sodium channel complex    A sodium channel in a cell membrane whose opening is governed by the membrane potential.

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    Lys A:1833 - Pro A:1834   [ RasMol ]  
    Pro A:1827 - Pro A:1828   [ RasMol ]  
 

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 Related Entries

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

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        SCN2A_HUMAN | Q992504jpz

(-) Related Entries Specified in the PDB File

1byy 1qg9