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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLIC HOMOLOGUE EXC-4 FROM C. ELEGANS
 
Authors :  S. J. Harrop, D. R. Littler, P. M. G. Curmi
Date :  10 Apr 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chloride Ion Channel, Clic, Gst Fold, Exc-4, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. R. Littler, S. J. Harrop, L. J. Brown, G. J. Pankhurst, A. V. Mynott, P. Luciani, R. A. Mandyam, M. Mazzanti, S. Tanda, M. A. Berryman, S. N. Breit, P. M. G. Curmi
Comparison Of Vertebrate And Invertebrate Clic Proteins: The Crystal Structures Of Caenorhabditis Elegans Exc-4 And Drosophila Melanogaster Dmclic
Proteins V. 71 364 2007
PubMed-ID: 17985355  |  Reference-DOI: 10.1002/PROT.21704
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHLORIDE INTRACELLULAR CHANNEL EXC-4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneEXC-4
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymEXCRETORY CANAL ABNORMAL PROTEIN 4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:77 , PRO A:79 , THR A:91 , ASN A:93 , HOH A:1086 , HOH A:1116BINDING SITE FOR RESIDUE CA A 1002
2AC2SOFTWAREGLN B:77 , PRO B:79 , THR B:91 , ASN B:93 , HOH B:1053 , HOH B:1147BINDING SITE FOR RESIDUE CA B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YV9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:78 -Pro A:79
2Pro B:78 -Pro B:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YV9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YV9)

(-) Exons   (0, 0)

(no "Exon" information available for 2YV9)

(-) 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:285
 aligned with EXC4_CAEEL | Q8WQA4 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:285
                             1                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     
           EXC4_CAEEL     - -MAEAYQIQSNGDPQSKPLLELYVKASGIDARRIGADLFCQEFWMELYALYEIGVARVEVKTVNVNSEAFKKNFLGAQPPIMIEEEKELTYTDNREIEGRIFHLAKEFNVPLFEKDPSAEKRIENLYRNFKLFLRAKVEFDKGKKEPSRVEDLPAQIKVHYNRVCEQLSNIDQLLSERKSRYLLGNSMTEYDCELMPRLHHIRIIGLSLLGFDIPHNFTHLWAYILTAYRTAAFIESCPADQDIIHHYKEQMNLFTNQRETLQSPTKTHTIPEKVLSDIRVKGLA 284
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......hhhhh.eeeeeee...........hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhh.....eeeehhhheee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh....hhhhhhh........hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv9 A   0 AMAEAYQIQSNGDPQSKPLLELYVKASGIDARRIGADLFCQEFWMELYALYEIGVARVEVKTVNVNSEAFKKNFLGAQPPIMIEEEKELTYTDNREIEGRIFHLAKEFNVPLFEKDPSAEKRIENLYRNFKLFLRAKVEFDKGKKEPSRVEDLPAQIKVHYNRVCEQLSNIDQLLSERKSRYLLGNSMTEYDCELMPRLHHIRIIGLSLLGFDIPHNFTHLWAYILTAYRTAAFIESCPADQDIIHHYKEQMNLFTNQRETLQSPTKTHTIPEKVLSDIRVKGLA 284
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with EXC4_CAEEL | Q8WQA4 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:271
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 
           EXC4_CAEEL    15 SKPLLELYVKASGIDARRIGADLFCQEFWMELYALYEIGVARVEVKTVNVNSEAFKKNFLGAQPPIMIEEEKELTYTDNREIEGRIFHLAKEFNVPLFEKDPSAEKRIENLYRNFKLFLRAKVEFDKGKKEPSRVEDLPAQIKVHYNRVCEQLSNIDQLLSERKSRYLLGNSMTEYDCELMPRLHHIRIIGLSLLGFDIPHNFTHLWAYILTAYRTAAFIESCPADQDIIHHYKEQMNLFTNQRETLQSPTKTHTIPEKVLSDIRVKGLAP 285
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...........hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhh.....eeeehhhheee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh-----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv9 B  15 SKPLLELYVKASGIDARRIGADLFCQEFWMELYALYEIGVARVEVKTVNVNSEAFKKNFLGAQPPIMIEEEKELTYTDNREIEGRIFHLAKEFNVPLFEKDPSAEKRIENLYRNFKLFLRAKVEFDK-----SRVEDLPAQIKVHYNRVCEQLSNIDQLLSERKSRYLLGNSMTEYDCELMPRLHHIRIIGLSLLGFDIPHNFTHLWAYILTAYRTAAFIESCPADQDIIHHYKEQMNLFTNQRETLQSPTKTHTIPEKVLSDIRVKGLAP 285
                                    24        34        44        54        64        74        84        94       104       114       124       134      |  -  |    154       164       174       184       194       204       214       224       234       244       254       264       274       284 
                                                                                                                                                        141   147                                                                                                                                          

   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 2YV9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YV9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YV9)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (EXC4_CAEEL | Q8WQA4)
molecular function
    GO:0005254    chloride channel activity    Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    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.
biological process
    GO:1902476    chloride transmembrane transport    The directed movement of chloride across a membrane.
    GO:0006821    chloride transport    The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0002064    epithelial cell development    The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    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: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:0035150    regulation of tube size    Ensuring that a tube is of the correct length and diameter. Tube size must be maintained not only during tube formation, but also throughout development and in some physiological processes.
    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:0043296    apical junction complex    A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0034707    chloride channel complex    An ion channel complex through which chloride ions pass.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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1k0m 2ahe 2yu7