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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PRIMARY CA2+ SENSOR OF THE NA+/CA2+ EXCHANGER
 
Authors :  J. Abramson, M. Sawaya
Date :  12 May 06  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium Sensory Domain, Beta-Sandwich, Cis-Proline, Beta- Bulge, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Nicoll, M. Sawaya, S. Kwon, D. Cascio, K. D. Philipson, J. Abramson
The Crystal Structure Of The Primary Ca2+ Sensor Of The Na+/Ca2+ Exchanger Reveals A Novel Ca2+ Binding Motif.
J. Biol. Chem. V. 281 21577 2006
PubMed-ID: 16774926  |  Reference-DOI: 10.1074/JBC.C600117200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SODIUM/CALCIUM EXCHANGER 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System CellM15PREP4
    Expression System PlasmidPQE32
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCA2+ BINDING DOMAIN 1
    Organism CommonDOG
    Organism ScientificCANIS LUPUS FAMILIARIS
    Organism Taxid9615
    StrainFAMILIARIS
    SynonymCBD1, NA+/CA2+ EXCHANGE PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GAI1Ligand/IonGUANIDINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:421 , GLU A:451 , GLU A:454BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREHOH A:1 , HOH A:15 , HOH A:16 , GLU A:385 , ASP A:421 , GLU A:451BINDING SITE FOR RESIDUE CA A 2001
3AC3SOFTWAREGLU A:385 , ASP A:447 , ILE A:449 , GLU A:451 , ASP A:498 , ASP A:500BINDING SITE FOR RESIDUE CA A 3001
4AC4SOFTWAREGLU A:385 , ASP A:446 , ASP A:447 , ASP A:499 , ASP A:500BINDING SITE FOR RESIDUE CA A 4001
5AC5SOFTWAREASP A:400 , THR A:402 , ASP A:453 , ASP A:498BINDING SITE FOR RESIDUE GAI A 1008
6AC6SOFTWAREHOH A:13 , PHE A:375 , PHE A:376 , GLU A:377 , THR A:411 , GLU A:412 , ASP A:413 , ALA A:418 , PRO A:489BINDING SITE FOR RESIDUE EPE A 1009

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:383 -A:387

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:488 -Pro A:489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DPK)

(-) Sequences/Alignments

Asymmetric/Biological 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:124
 aligned with NAC1_CANLF | P23685 from UniProtKB/Swiss-Prot  Length:970

    Alignment length:144
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530    
           NAC1_CANLF   391 HEVNTEVAENDPVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDENFLVHLSNVKVSSEASEDGILEANHVSALACLGSPSTATVTIFDDDHA 534
               SCOP domains ---        d2dpka1 A:370-502 Sodium/calcium exchanger 1                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...--------..eeeee...eeeee....eeeeeeeee.......eeeeeeee.............eeeeee.....eeeeeee..........eeeeeeeeeeee...------------...eee....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dpk A 367 HGI--------PVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDENFLVHLSNVKVSSE------------SALACLGSPSTATVTIFDDDHA 502
                              |      - |     378       388       398       408       418       428       438       448       458       468         -  |    488       498    
                              |      370                                                                                               468          481                     
                            369                                                                                                                                             

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NAC1_CANLF | P23685)
molecular function
    GO:0030506    ankyrin binding    Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins.
    GO:0015297    antiporter activity    Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005432    calcium:sodium antiporter activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + Na+(out) = Ca2+(out) + Na+(in).
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:1901660    calcium ion export    The directed movement of calcium ion out of a cell or organelle.
    GO:0070509    calcium ion import    The directed movement of calcium ions into a cell or organelle.
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007154    cell communication    Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
    GO:0034614    cellular response to reactive oxygen species    Any process that results in a change in state or activity of a cell (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.
    GO:0006883    cellular sodium ion homeostasis    Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell.
    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:0030501    positive regulation of bone mineralization    Any process that activates or increases the frequency, rate or extent of bone mineralization.
    GO:0098735    positive regulation of the force of heart contraction    Any process that increases the force of heart muscle contraction.
    GO:0035994    response to muscle stretch    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 myofibril being extended beyond its slack length.
    GO:0071436    sodium ion export    The directed movement of sodium ions out of a cell or organelle.
    GO:0097369    sodium ion import    The directed movement of sodium ions into a cell or organelle.
    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: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: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: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:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAC1_CANLF | P236852fws 2fwu 2qvk 2qvm 3gin 3us9

(-) Related Entries Specified in the PDB File

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