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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED HOMO SAPIENS CLIC3
 
Authors :  D. R. Littler, P. M. G. Curmi, S. N. Breit, A. Perrakis
Date :  04 Nov 09  (Deposition) - 17 Nov 09  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gst, Glutathione, Clic, Chloride Channel, Chloride Intracel, Chloride, Cytoplasm, Ion Transport, Ionic Channel, Nucleus, Polymorphism, Transport, Voltage-Gated Channel, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. R. Littler, L. J. Brown, S. N. Breit, A. Perrakis, P. M. G. Curmi
Structure Of Human Clic3 At 2 A Resolution
Proteins V. 78 1594 2010
PubMed-ID: 20146363  |  Reference-DOI: 10.1002/PROT.22675

(-) Compounds

Molecule 1 - CHLORIDE INTRACELLULAR CHANNEL PROTEIN 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28-LIC
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-230
    GeneCLIC3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:27 , LEU A:76 , HOH A:239 , HOH A:265 , LYS B:111 , GLN B:130BINDING SITE FOR RESIDUE SO4 A 231
2AC2SOFTWAREHIS A:221 , SER A:222 , PRO B:196 , ALA B:197 , GLU B:198BINDING SITE FOR RESIDUE SO4 A 232
3AC3SOFTWARELYS A:111 , HOH A:236 , ARG B:27 , LEU B:76BINDING SITE FOR RESIDUE SO4 A 233
4AC4SOFTWAREARG A:97 , HIS A:148 , GLY A:166 , ASP A:167 , ARG A:168 , HOH A:253BINDING SITE FOR RESIDUE SO4 A 234
5AC5SOFTWAREPHE A:109 , HIS A:110 , LYS A:179 , HOH A:245 , HIS B:110BINDING SITE FOR RESIDUE SO4 A 235
6AC6SOFTWAREHIS A:110 , HIS B:110 , LYS B:179 , HOH B:250BINDING SITE FOR RESIDUE SO4 B 231
7AC7SOFTWAREARG B:133 , ARG B:137 , HOH B:289BINDING SITE FOR RESIDUE SO4 B 232

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KJY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:62 -Pro A:63
2Pro A:88 -Pro A:89
3Leu B:62 -Pro B:63
4Pro B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020424P38HCLIC3_HUMANPolymorphism2292923A/BP38H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020424P38HCLIC3_HUMANPolymorphism2292923AP38H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020424P38HCLIC3_HUMANPolymorphism2292923BP38H

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.CLIC3_HUMAN68-235
 
  2A:68-230
B:68-230
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.CLIC3_HUMAN68-235
 
  1A:68-230
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.CLIC3_HUMAN68-235
 
  1-
B:68-230

(-) Exons   (0, 0)

(no "Exon" information available for 3KJY)

(-) Sequences/Alignments

Asymmetric 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:223
 aligned with CLIC3_HUMAN | O95833 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:233
                               1                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
          CLIC3_HUMAN     - ---MAETKLQLFVKASEDGESVGHCPSCQRLFMVLLLKGVPFTLTTVDTRRSPDVLKDFAPGSQLPILLYDSDAKTDTLQIEDFLEETLGPPDFPSLAPRYRESNTAGNDVFHKFSAFIKNPVPAQDEALYQQLLRALARLDSYLRAPLEHELAGEPQLRESRRRFLDGDRLTLADCSLLPKLHIVDTVCAHFRQAPIPAELRGVRRYLDSAMQEKEFKYTCPHSAEILAAYR 230
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeee..........hhhhhhhhhhhhhhh..eeeeee.----------........eeee..eee.hhhhhhhhhhhhh...........hhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------GST_CTER  PDB: A:68-230 UniProt: 68-235                                                                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kjy A  -8 LEVLFQTKLQLFVKASEDGESVGHCPSCQRLFMVLLLKGVPFTLTTVD----------FAPGSQLPILLYDSDAKTDTLQIEDFLEETLGPPDFPSLAPRYRESNTAGNDVFHKFSAFIKNPVPAQDEALYQQLLRALARLDSYLRAPLEHELAGEPQLRESRRRFLDGDRLTLADCSLLPKLHIVDTVCAHFRQAPIPAELRGVRRYLDSAMQEKEFKYTCPHSAEILAAYR 230
                                 ||  7        17        27        37       | -        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
                                -3|                                       45         56                                                                                                                                                                              
                                  4                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with CLIC3_HUMAN | O95833 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:233
                               1                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
          CLIC3_HUMAN     - ---MAETKLQLFVKASEDGESVGHCPSCQRLFMVLLLKGVPFTLTTVDTRRSPDVLKDFAPGSQLPILLYDSDAKTDTLQIEDFLEETLGPPDFPSLAPRYRESNTAGNDVFHKFSAFIKNPVPAQDEALYQQLLRALARLDSYLRAPLEHELAGEPQLRESRRRFLDGDRLTLADCSLLPKLHIVDTVCAHFRQAPIPAELRGVRRYLDSAMQEKEFKYTCPHSAEILAAYR 230
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------GST_C_2-3kjyB01 B:75-208                                                                                                              ---------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------GST_C_2-3kjyB02 B:75-208                                                                                                              ---------------------- Pfam domains (2)
           Pfam domains (3) --------------------GST_N_3-3kjyB03 B:18-90                                                  -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------GST_N_3-3kjyB04 B:18-90                                                  -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeee...eeeeee..........hhhhhhhhhhhhhhh..eeeeee.-------------.....eeee..eee.hhhhhhhhhhhhh...........hhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------GST_CTER  PDB: B:68-230 UniProt: 68-235                                                                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kjy B  -8 LEVLFQGKLQLFVKASEDGESVGHCPSCQRLFMVLLLKGVPFTLTTVD-------------GSQLPILLYDSDAKTDTLQIEDFLEETLGPPDFPSLAPRYRESNTAGNDVFHKFSAFIKNPVPAQDEALYQQLLRALARLDSYLRAPLEHELAGEPQLRESRRRFLDGDRLTLADCSLLPKLHIVDTVCAHFRQAPIPAELRGVRRYLDSAMQEKEFKYTCPHSAEILAAYR 230
                                  || 7        17        27        37       | -         - |      67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
                                 -2|                                      45            59                                                                                                                                                                           
                                   5                                                                                                                                                                                                                                 

   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 3KJY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KJY)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: GST_C (118)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CLIC3_HUMAN | O95833)
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: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: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: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: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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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
        CLIC3_HUMAN | O958333fy7

(-) Related Entries Specified in the PDB File

3fy7 STRUCTURE OF OXIDISED CLIC3