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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC FRAC (SECOND CRYSTAL FORM)
 
Authors :  J. M. M. Caaveiro, K. Tanaka, K. Tsumoto
Date :  09 Apr 13  (Deposition) - 09 Apr 14  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Sandwich, Amphipathic Alpha-Helix, Actinoporin, Pore-Forming Toxin, Cytolysin, Membrane Lipids, Secreted Protein, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tanaka, J. M. M. Caaveiro, K. Morante, J. M. Gonzalez-Manas, K. Tsumoto
Structural Basis For Self-Assembly Of A Cytolytic Pore Line By Protein And Lipid
Nat Commun V. 6 6337 2015
PubMed-ID: 25716479  |  Reference-DOI: 10.1038/NCOMMS7337
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRAGACEATOXIN C
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEM-T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FRAC
    Organism Common: STRAWBERRY ANEMONE
    Organism Scientific: ACTINIA FRAGACEA
    Organism Taxid: 396334
    Synonym: FRAC

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3W9P)

(-) Sites  (0, 0)

(no "Site" information available for 3W9P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W9P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W9P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W9P)

(-) Exons   (0, 0)

(no "Exon" information available for 3W9P)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:175
 aligned with ACTPC_ACTFR | B9W5G6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:175
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     
          ACTPC_ACTFR     5 AGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w9p A   5 AGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with ACTPC_ACTFR | B9W5G6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:174
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175    
          ACTPC_ACTFR     6 GAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w9p B   6 GAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
   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 3W9P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W9P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W9P)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACTPC_ACTFR | B9W5G6)
molecular function
    GO:0015267    channel activity    Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
biological process
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
    GO:0052331    hemolysis in other organism involved in symbiotic interaction    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another, where two organisms are in a symbiotic interaction.
    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:0046931    pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a pore complex. A pore complex is a small opening in a membrane that allows the passage of liquids and/or gases.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0042151    nematocyst    An organelle found in cnidoblast (nematoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the cnidocyst) is stimulated by a prey or another stimulus.
    GO:0044218    other organism cell membrane    The cell membrane of a secondary organism with which the first organism is interacting.
    GO:0044279    other organism membrane    A membrane of a secondary organism with which the first organism is interacting.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACTPC_ACTFR | B9W5G6: 3lim 3vwi 3zwg 3zwj 4tsl 4tsn 4tso 4tsp 4tsq 4tsy 4wdc 5bpg 5gwf

(-) Related Entries Specified in the PDB File

3lim
3vwi MONOMER IN DIFFERENT CRYSTAL FORM