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(-) Description

Title :  STRUCTURE OF HUMAN CLIC2, CRYSTAL FORM A
 
Authors :  G. Hansen, B. A. Cromer, M. A. Gorman, M. W. Parker
Date :  02 Sep 07  (Deposition) - 13 Nov 07  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Chloride Intracellular Channels, Clic2, Pore-Forming Protein, Ryanodine Receptor, Chloride Channel, Ion Transport, Ionic Channel, Transport, Voltage-Gated Channel, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Cromer, M. A. Gorman, G. Hansen, J. J. Adams, M. Coggan, D. R. Littler, L. J. Brown, M. Mazzanti, S. N. Breit, P. M. G. Curmi, A. F. Dulhunty, P. G. Board, M. W. Parker
Structure Of The Janus Protein Human Clic2
J. Mol. Biol. V. 374 719 2007
PubMed-ID: 17945253  |  Reference-DOI: 10.1016/J.JMB.2007.09.041

(-) Compounds

Molecule 1 - CHLORIDE INTRACELLULAR CHANNEL PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypeINHOUSE VECTOR
    GeneCLIC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymXAP121

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:25 , SER A:26 , ILE A:27 , PHE A:37 , TRP A:41 , THR A:51 , HIS A:227 , HOH A:330 , HOH A:347BINDING SITE FOR RESIDUE GSH A 248
2AC2SOFTWAREPRO A:97 , ARG A:98 , TYR A:99 , PRO A:100 , HIS A:101 , ALA A:131 , ASN A:134 , PHE A:135 , GLN A:178 , HOH A:328 , HOH A:372BINDING SITE FOR RESIDUE GSH A 249

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:33

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:70 -Pro A:71
2Pro A:96 -Pro A:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068898H101QCLIC2_HUMANDisease (MRXS32)398122917AH101Q

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.CLIC2_HUMAN76-239  1A:76-239

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003694491cENSE00001890277X:154563955-154563680276CLIC2_HUMAN1-19191A:10-1910
1.3ENST000003694493ENSE00001620246X:154528458-154528349110CLIC2_HUMAN20-56371A:20-5536
1.4ENST000003694494ENSE00001096470X:154528223-154528098126CLIC2_HUMAN56-98431A:66-9833
1.5ENST000003694495ENSE00001023655X:154509357-154509251107CLIC2_HUMAN98-134371A:98-13437
1.6cENST000003694496cENSE00001096460X:154508619-154508438182CLIC2_HUMAN134-194611A:134-19461
1.8cENST000003694498cENSE00001847718X:154507353-1545055001854CLIC2_HUMAN195-247531A:195-24551

(-) 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:226
 aligned with CLIC2_HUMAN | O15247 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:236
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239      
          CLIC2_HUMAN    10 VDPEIELFVKAGSDGESIGNCPFCQRLFMILWLKGVKFNVTTVDMTRKPEELKDLAPGTNPPFLVYNKELKTDFIKIEEFLEQTLAPPRYPHLSPKYKESFDVGCNLFAKFSAYIKNTQKEANKNFEKSLLKEFKRLDDYLNTPLLDEIDPDSAEEPPVSRRLFLDGDQLTLADCSLLPKLNIIKVAAKKYRDFDIPAEFSGVWRYLHNAYAREEFTHTCPEDKEIENTYANVAKQ 245
               SCOP domains d2r4va1 A:10-97 automated matches                                                       d2r4va2 A:98-245 automated matches                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------GST_C_2-2r4vA01 A:75-218                                                                                                                        --------------------------- Pfam domains (1)
           Pfam domains (2) ----------------GST_N_3-2r4vA02 A:26-98                                                  --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee..........hhhhhhhhhhhhhhh...eeeee...----------......eeee..eee.hhhhhhhhhhhhh............hhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------GST_CTER  PDB: A:76-239 UniProt: 76-239                                                                                                                             ------ PROSITE
           Transcript 1 (1) Exon 1.1c Exon 1.3  PDB: A:20-55 UniProt: 20-56-----------------------------------------Exon 1.5  PDB: A:98-134              ------------------------------------------------------------Exon 1.8c  PDB: A:195-245 UniProt: 195-247          Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.4  PDB: A:66-98 UniProt: 56-98      -----------------------------------Exon 1.6c  PDB: A:134-194 UniProt: 134-194                   --------------------------------------------------- Transcript 1 (2)
                 2r4v A  10 VDPEIELFVKAGSDGESIGNCPFCQRLFMILWLKGVKFNVTTVDMT----------PGTNPPFLVYNKELKTDFIKIEEFLEQTLAPPRYPHLSPKYKESFDVGCNLFAKFSAYIKNTQKEANKNFEKSLLKEFKRLDDYLNTPLLDEIDPDSAEEPPVSRRLFLDGDQLTLADCSLLPKLNIIKVAAKKYRDFDIPAEFSGVWRYLHNAYAREEFTHTCPEDKEIENTYANVAKQ 245
                                    19        29        39        49     |   -      | 69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239      
                                                                        55         66                                                                                                                                                                                   

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R4V)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: GST_C (118)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLIC2_HUMAN | O15247)
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:0004602    glutathione peroxidase activity    Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
    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: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: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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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: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:0060315    negative regulation of ryanodine-sensitive calcium-release channel activity    Any process that decreases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
    GO:0051099    positive regulation of binding    Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
    GO:0010881    regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion    Any process that modulates the frequency, rate or extent of cardiac muscle contraction via the regulation of the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol. The sarcoplasmic reticulum is the endoplasmic reticulum of striated muscle, specialised for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction.
    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:0010880    regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum    Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
    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: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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        CLIC2_HUMAN | O152472per 2r5g

(-) Related Entries Specified in the PDB File

2r5g