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(-) Description

Title :  STRUCTURE OF THE C-DOMAIN OF CALCIUM-SATURATED CALMODULIN BOUND TO THE IQ MOTIF OF NAV1.2
 
Authors :  C. A. Fowler, M. D. Feldkamp, L. Yu, M. A. Shea
Date :  21 Feb 13  (Deposition) - 23 Jul 14  (Release) - 19 Apr 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (21x)
NMR Structure *:  A,B  (1x)
Keywords :  Calcium Binding Protein, Nav1. 2, Ion Channel Gating, Iq Motif, Metal Binding, Sodium Channels, Metal Transport, Voltage Dependent, Voltage Gated, Calcium Binding Protein-Metal Transport Complex, Neuronal Peptides, Ef-Hand, Calcium-Binding Protein-Metal Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Hovey, C. A. Fowler, R. Mahling, Z. Lin, M. S. Miller, D. C. Marx, J. B. Yoder, E. H. Kim, K. M. Tefft, B. C. Waite, M. D. Feldkamp, L. Yu, M. A. Shea
Calcium Triggers Reversal Of Calmodulin On Nested Anti-Parallel Sites In The Iq Motif Of The Neuronal Voltage-Dependent Sodium Channel Nav1. 2.
Biophys. Chem. V. 224 1 2017
PubMed-ID: 28343066  |  Reference-DOI: 10.1016/J.BPC.2017.02.006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALMODULIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 77-149
    GeneCAM, GSPATT00015825001
    Organism ScientificPARAMECIUM TETRAURELIA
    Organism Taxid5888
    StrainD4-2
    SynonymCAM
 
Molecule 2 - SODIUM CHANNEL PROTEIN TYPE 2 SUBUNIT ALPHA
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 1901-1927
    GeneSCN2A, SCN2A1
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymSODIUM CHANNEL PROTEIN BRAIN II SUBUNIT ALPHA, SODIUM CHANNEL PROTEIN TYPE II SUBUNIT ALPHA, VOLTAGE-GATED SODIUM CHANNEL SUBUNIT ALPHA NAV1.2

 Structural Features

(-) Chains, Units

  12
NMR Structure (21x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:93 , ASP A:95 , ASN A:97 , LEU A:99 , GLU A:104BINDING SITE FOR RESIDUE CA A 2001
2AC2SOFTWAREASP A:129 , ASP A:131 , ASP A:133 , HIS A:135 , GLU A:140BINDING SITE FOR RESIDUE CA A 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M5E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M5E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M5E)

(-) PROSITE Motifs  (3, 5)

NMR Structure (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM_PARTE8-43
44-79
81-116
117-149
  2-
-
A:80-115
A:116-148
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM_PARTE21-33
57-69
94-106
130-142
  2-
-
A:93-105
A:129-141
3IQPS50096 IQ motif profile.SCN2A_RAT1905-1934  1B:1905-1927
NMR Structure * (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM_PARTE8-43
44-79
81-116
117-149
  2-
-
A:80-115
A:116-148
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM_PARTE21-33
57-69
94-106
130-142
  2-
-
A:93-105
A:129-141
3IQPS50096 IQ motif profile.SCN2A_RAT1905-1934  1B:1905-1927

(-) Exons   (0, 0)

(no "Exon" information available for 2M5E)

(-) 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:73
 aligned with CALM_PARTE | P07463 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:73
                                    86        96       106       116       126       136       146   
          CALM_PARTE     77 MKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGEKLTDDEVDEMIREADIDGDGHINYEEFVRMMVSK  149
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_-EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (1)
                PROSITE (2) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------- Transcript
                2m5e A   76 MKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGEKLTDDEVDEMIREADIDGDGHINYEEFVRMMVSK  148
                                    85        95       105       115       125       135       145   

Chain B from PDB  Type:PROTEIN  Length:27
 aligned with SCN2A_RAT | P04775 from UniProtKB/Swiss-Prot  Length:2005

    Alignment length:27
                                  1910      1920       
           SCN2A_RAT   1901 KRKQEEVSAIVIQRAYRRYLLKQKVKK 1927
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE ----IQ  PDB: B:1905-1927    PROSITE
                 Transcript --------------------------- Transcript
                2m5e B 1901 KRKQEEVSAIVIQRAYRRYLLKQKVKK 1927
                                  1910      1920       

   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 2M5E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M5E)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (CALM_PARTE | P07463)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain B   (SCN2A_RAT | P04775)
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:0043522    leucine zipper domain binding    Interacting selectively and non-covalently with a leucine zipper domain, a protein secondary structure exhibiting a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns.
    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: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:0031402    sodium ion binding    Interacting selectively and non-covalently with sodium ions (Na+).
    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: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: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:0043194    axon initial segment    Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment.
    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: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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        CALM_PARTE | P074631clm 1exr 1n0y 1osa 2kxw 5e1k 5e1n 5e1p
        SCN2A_RAT | P047751byy 2kxw

(-) Related Entries Specified in the PDB File

1exr THE 1.0 ANGSTROM CRYSTAL STRUCTURE OF CA2+-BOUND CALMODULIN RELATED ID: 19050 RELATED DB: BMRB
2kxw STRUCTURE OF THE C-DOMAIN FRAGMENT OF APO-CALMODULIN BOUND TO THE IQ MOTIF OF NAV1.2