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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VIBRIO CHOLERAE CYTOLYSIN (HLYA) PRO-TOXIN WITH OCTYLGLUCOSIDE BOUND
 
Authors :  R. Olson, E. Gouaux
Date :  13 Sep 04  (Deposition) - 14 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Pore-Forming Toxin, Hemolysin, Cytolysin, Pro-Toxin, Water- Soluble Monomer, Beta-Prism, Beta-Trefoil (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Olson, E. Gouaux
Crystal Structure Of The Vibrio Cholerae Cytolysin (Vcc) Pro-Toxin And Its Assembly Into A Heptameric Transmembrane Pore
J. Mol. Biol. V. 350 997 2005
PubMed-ID: 15978620  |  Reference-DOI: 10.1016/J.JMB.2005.05.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOLYSIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-PARALLEL2
    Expression System Strain: ORIGAMI B (NOVAGEN)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HLYA
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: O1 EL TOR 8731
    Synonym: CYTOLYSIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BOG1Ligand/IonB-OCTYLGLUCOSIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:362 , GLY A:613 , ALA A:614 , ALA A:615 , ASP A:617 , GLY A:631 , GLY A:632 , TYR A:654 , HOH A:1225BINDING SITE FOR RESIDUE BOG A 999

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:157 -A:175
2A:472 -A:486
3A:512 -A:524

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:271 -Pro A:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_HLYA_VIBCH_001 *S453FHLYA_VIBCH  ---  ---AS428F
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.HLYA_VIBCH484-575  1A:459-550

(-) Exons   (0, 0)

(no "Exon" information available for 1XEZ)

(-) 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:663
 aligned with HLYA_VIBCH | P09545 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:696
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735      
           HLYA_VIBCH    46 AIKYYNAADWQAEDNALPSLAELRDLVINQQKRVLVDFSQISDAEGQAEMQAQFRKAYGVGFANQFIVITEHKGELLFTPFDQAEEVDPQLLEAPRTARLLARSGFASPAPANSETNTLPHVAFYISVNRAISDEECTFNNSWLWKNEKGSRPFCKDANISLIYRVNLERSLQYGIVGSATPDAKIVRISLDDDSTGAGIHLNDQLGYRQFGASYTTLDAYFREWSTDAIAQDYRFVFNASNNKAQILKTFPVDNINEKFERKEVSGFELGVTGGVEVSGDGPKAKLEARASYTQSRWLTYNTQDYRIERNAKNAQAVSFTWNRQQYATAESLLNRSTDALWVNTYPVDVNRISPLSYASFVPKMDVIYKASATETGSTDFIIDSSVNIRPIYNGAYKHYYVVGAHQSYHGFEDTPRRRITKSASFTVDWDHPVFTGGRPVNLQLASFNNRCIQVDAQGRLAANTCDSQQSAQSFIYDQLGRYVSASNTKLCLDGEALDALQPCNQNLTQRWEWRKGTDELTNVYSGESLGHDKQTGELGLYASSNDAVSLRTITAYTDVFNAQESSPILGYTQGKMNQQRVGQDHRLYVRAGAAIDALGSASDLLVGGNGGSLSSVDLSGVKSITATSGDFQYGGQQLVALTFTYQDGRQQTVGSKAYVTNAHEDRFDLPAAAKITQLKIWSDDWLVKGVQFDLN 741
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Hemolysin_N-    1xezA02 A:21-162                                                                                                              ---------------------------Leukocidin-1xezA03 A:190-452                                                                                                                                                                                                                                           -------Ricin_B_lectin-1xezA01 A:460-574                                                                                   ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhh----..hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh......eeeeeee..eeeeeee....-----------------------------......eeeeeeeeeee......eee..........eee.....eeeeeeeeeeeee............eeeeeeee.......eee......eeeee.......eeeeeeeeeeeeeeeeeeeee.....eeeeee.........eeeeeeeeeeee........hhhhh.....eeeeeeeeeeee...eeeeee......eeeeeee.....hhhhh...ee.........hhhhhhhhhh......eeeeeeee.....eeeeeeeeeeeeeeeeeeeeeee....eeeeeeee.....eeeeeeeeeeee..hhhhhh...eeeee.....eeeee.....eeee.....hhhh.eee.....eee..eeeee.........ee...hhhh.eee......eee.....eeeee.....eeee......ee..eeeee............ee....eeeeee.....eeeeee...eeeee......ee....eeeeee...eeeeeeeeeee....eeeeeeeeee....eeeee....eeeeeeeeee......eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RICIN_B_LECTIN  PDB: A:459-550 UniProt: 484-575                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xez A  21 AIKYYNAADWQA----LPSLAELRDLVINQQKRVLVDFSQISDAEGQAEMQAQFRKAYGVGFANQFIVITEHKGELLFTPFDRTE-----------------------------ETNTLPHVAFYISVNRAISDEECTFNNSWLWKNEKGSRPFCKDANISLIYRVNLERSLQYGIVGSATPDAKIVRISLDDDSTGAGIHLNDQLGYRQFGASYTTLDAYFREWSTDAIAQDYRFVFNASNNKAQILKTFPVDNINEKFERKEVSGFELGVTGGVEVSGDGPKAKLEARASYTQSRWLTYNTQDYRIERNAKNAQAVSFTWNRQQYATAESLLNRSTDALWVNTYPVDVNRISPLSYASFVPKMDVIYKASATETGSTDFIIDSSVNIRPIYNGAYKHYYVVGAHQSYHGFEDTPRRRITKSASFTVDWDHPVFTGGRPVNLQLASFNNRCIQVDAQGRLTANMCDSQQSAQSFIYDQLGRYVSASNTKLCLDGAALDALQPCNQNLTQRWEWRKGTDELTNVYSGESLGHDKQTGELGLYASSNDAVSLRTITAYTDVFNAQESSPILGYTQGKMNQQRVGQDNRLYVRAGAAIDALGSASDLLVGGNGGSLSSVDLSGVKSITATSGDFQYGGQQLVALTFTYQDGRQQTVGSKAYVTNAHEDRFDLPDAAKITQLKIWADDWLVKGVQFDLN 716
                                    30 |    | 40        50        60        70        80        90       100    |    -         -         -    |  140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710      
                                      32   37                                                                 105                           135
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1XEZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XEZ)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)
(-)
Clan: no clan defined [family: Hemolysin_N] (1)
(-)
Clan: no clan defined [family: Leukocidin] (9)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HLYA_VIBCH | P09545)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0051715    cytolysis in other organism    The killing by an organism of a cell in another organism by means of 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.
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:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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.

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