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(-) Description

Title :  STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN F COMPONENT FROM STAPHYLOCOCCUS AUREUS
 
Authors :  J. D. Pedelacq, L. Mourey, L. Maveyraud, G. Prevost, J. P. Samama
Date :  12 Jan 99  (Deposition) - 15 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Bi-Component Leucotoxin, Transmembrane Pore (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Pedelacq, L. Maveyraud, G. Prevost, L. Baba-Moussa, A. Gonzalez, E. Courcelle, W. Shepard, H. Monteil, J. P. Samama, L. Mourey
The Structure Of A Staphylococcus Aureus Leucocidin Component (Lukf-Pv) Reveals The Fold Of The Water-Soluble Species Of A Family Of Transmembrane Pore-Forming Toxins.
Structure Fold. Des. V. 7 277 1999
PubMed-ID: 10368297  |  Reference-DOI: 10.1016/S0969-2126(99)80038-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCOCIDIN
    Atcc: ATCC 49775
    Cellular Location: CHROMOSOME
    Chains: A
    Collection: ATCC 49775
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: V8
    Synonym: LUKF-PV

 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
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:173 , TRP A:176 , TYR A:179 , GLU A:191 , GLY A:195 , SER A:196 , ARG A:197 , HOH A:502 , HOH A:541BINDING SITE FOR RESIDUE MES A 401
2AC2SOFTWARETHR A:71 , ILE A:72 , SER A:199 , ASN A:200 , ASN A:202 , ALA A:203 , TRP A:256 , TRP A:261BINDING SITE FOR RESIDUE MES A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PVL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:100 -Pro A:101
2Gly A:177 -Pro A:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PVL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PVL)

(-) Exons   (0, 0)

(no "Exon" information available for 1PVL)

(-) 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:298
 aligned with O50604_STAAU | O50604 from UniProtKB/TrEMBL  Length:325

    Alignment length:301
                                    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       294       304       314       324 
         O50604_STAAU    25 AQHITPVSEKKVDDKITLYKTTATSDSDKLKISQILTFNFIKDKSYDKDTLILKAAGNIYSGYTKPNPKDTISSQFYWGSKYNISINSDSNDSVNVVDYAPKNQNEEFQVQQTVGYSYGGDINISNGLSGGGNGSKSFSETINYKQESYRTSLDKRTNFKKIGWDVEAHKIMNNGWGPYGRDSYHSTYGNEMFLGSRQSNLNAGQNFLEYHKMPVLSRGNFNPEFIGVLSRKQNAAKKSKITVTYQREMDRYTNFWINFNWIGNNYKDENRATHTSIYEVDWENHTVKLIDTQSKEKNPMS 325
               SCOP domains d1pvla_ A: Leucocidin K component LukF-PV                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1pvlA00 A:1-301 Leukocidin-like                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------Leukocidin-1pvlA01 A:34-284                                                                                                                                                                                                                                ----------------- Pfam domains
         Sec.struct. author eeeeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee..eeeee.....eeeeeee.eeeeeeeee....eeeeeee..eee...eeeeeeeeee..eeeeee......---..eeeeeeeeee.eeeee...ee..eeeeeeee.eeee....eee.....................hhhhh..hhhhhhhhhhheeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee...eeeeeeee..eeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvl A   1 AQHITPVSEKKVDDKITLYKTTATSDSDKLKISQILTFNFIKDKSYDKDTLILKAAGNIYSGYTKPNPKDTISSQFYWGSKYNISINSDSNDSVNVVDYAPKNQNEEFQVQQTVGYSYGGDINISNGLSGGG---KSFSETINYKQESYRTSLDKRTNFKKIGWDVEAHKIMNNGWGPYGRDSYHSTYGNEMFLGSRQSNLNAGQNFLEYHKMPVLSRGNFNPEFIGVLSRKQNAAKKSKITVTYQREMDRYTNFWNQLHWIGNNYKDENRATHTSIYEVDWENHTVKLIDTQSKEKNPMS 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 |   | 140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                                                                                                                                             132 136                                                                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:298
 aligned with Q5FBD2_STAAU | Q5FBD2 from UniProtKB/TrEMBL  Length:325

    Alignment length:301
                                    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       294       304       314       324 
         Q5FBD2_STAAU    25 AQHITPVSEKKVDDKITLYKTTATSDSDKLKISQILTFNFIKDKSYDKDTLILKAAGNIYSGYTKPNPKDTISSQFYWGSKYNISINSDSNDSVNVVDYAPKNQNEEFQVQQTVGYSYGGDINISNGLSGGGNGSKSFSETINYKQESYRTSLDKRTNFKKIGWDVEAHKIMNNGWGPYGRDSYHSTYGNEMFLGSRQSNLNAGQNFLEYHKMPVLSRGNFNPEFIGVLSRKQNAAKKSKITVTYQREMDRYTNFWNQLHWIGNNYKDENRATHTSIYEVDWENHTVKLIDTQSKEKNPMS 325
               SCOP domains d1pvla_ A: Leucocidin K component LukF-PV                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1pvlA00 A:1-301 Leukocidin-like                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------Leukocidin-1pvlA01 A:34-284                                                                                                                                                                                                                                ----------------- Pfam domains
         Sec.struct. author eeeeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee..eeeee.....eeeeeee.eeeeeeeee....eeeeeee..eee...eeeeeeeeee..eeeeee......---..eeeeeeeeee.eeeee...ee..eeeeeeee.eeee....eee.....................hhhhh..hhhhhhhhhhheeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee...eeeeeeee..eeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvl A   1 AQHITPVSEKKVDDKITLYKTTATSDSDKLKISQILTFNFIKDKSYDKDTLILKAAGNIYSGYTKPNPKDTISSQFYWGSKYNISINSDSNDSVNVVDYAPKNQNEEFQVQQTVGYSYGGDINISNGLSGGG---KSFSETINYKQESYRTSLDKRTNFKKIGWDVEAHKIMNNGWGPYGRDSYHSTYGNEMFLGSRQSNLNAGQNFLEYHKMPVLSRGNFNPEFIGVLSRKQNAAKKSKITVTYQREMDRYTNFWNQLHWIGNNYKDENRATHTSIYEVDWENHTVKLIDTQSKEKNPMS 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 |   | 140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                                                                                                                                             132 136
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5FBD2_STAAU | Q5FBD2)
biological process
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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.

Chain A   (O50604_STAAU | O50604)
biological process
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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.

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