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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CELL-BINDING B OLIGOMER OF VEROTOXIN-1 FROM E. COLI
 
Authors :  P. E. Stein, A. Boodhoo, G. J. Tyrrell, J. L. Brunton, R. D. Oeffner, G. Bu R. J. Read
Date :  27 Sep 10  (Deposition) - 13 Oct 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. E. Stein, A. Boodhoo, G. J. Tyrrell, J. L. Brunton, R. J. Read
Crystal Structure Of The Cell-Binding B Oligomer Of Verotoxin-1 From E. Coli.
Nature V. 355 748 1992
PubMed-ID: 1741063  |  Reference-DOI: 10.1038/355748A0

(-) Compounds

Molecule 1 - SHIGA-LIKE TOXIN 1 SUBUNIT B
    Chains: A, B, C, D, E
    Fragment: RESIDUES 21-89
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: TB1 (PJLB 120)
    Synonym: SLT-1 B SUBUNIT, SLT-1B, SLT-IB, VEROCYTOTOXIN 1 SUBUNIT B, VEROTOXIN 1 SUBUNIT B

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:1 , HOH B:2027 , HOH B:2028 , THR D:1BINDING SITE FOR RESIDUE ZN B1070
2AC2SOFTWARETHR C:1 , GLU C:65 , HOH C:2039BINDING SITE FOR RESIDUE ZN C1070
3AC3SOFTWARETHR E:1BINDING SITE FOR RESIDUE ZN E1070

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:57
2B:4 -B:57
3C:4 -C:57
4D:4 -D:57
5E:4 -E:57

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XSC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XSC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XSC)

(-) Exons   (0, 0)

(no "Exon" information available for 2XSC)

(-) 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:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH19   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xsca_ A: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee.hhhhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc A  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain A from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH30   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xsca_ A: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee.hhhhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc A  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH19   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xscb_ B: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee.hhhhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc B  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH30   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xscb_ B: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee.hhhhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc B  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH19   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xscc_ C: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc C  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH30   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xscc_ C: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc C  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH19   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xscd_ D: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc D  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH30   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xscd_ D: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc D  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain E from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH19   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xsce_ E: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
           Pfam domains (1) SLT_beta-2xscE01 E:1-69                                               Pfam domains (1)
           Pfam domains (2) SLT_beta-2xscE02 E:1-69                                               Pfam domains (2)
           Pfam domains (3) SLT_beta-2xscE03 E:1-69                                               Pfam domains (3)
           Pfam domains (4) SLT_beta-2xscE04 E:1-69                                               Pfam domains (4)
           Pfam domains (5) SLT_beta-2xscE05 E:1-69                                               Pfam domains (5)
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc E  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60         


Chain E from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
            STXB_BPH30   21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 89
               SCOP domains d2xsce_ E: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
           Pfam domains (1) SLT_beta-2xscE01 E:1-69                                               Pfam domains (1)
           Pfam domains (2) SLT_beta-2xscE02 E:1-69                                               Pfam domains (2)
           Pfam domains (3) SLT_beta-2xscE03 E:1-69                                               Pfam domains (3)
           Pfam domains (4) SLT_beta-2xscE04 E:1-69                                               Pfam domains (4)
           Pfam domains (5) SLT_beta-2xscE05 E:1-69                                               Pfam domains (5)
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2xsc E  1 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 69
                                    10        20        30        40        50        60
   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, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0 ; only for superseded entry 1BOV: 1,5)

(no "CATH Domain" information available for 2XSC, only for superseded entry 1BOV replaced by 2XSC)

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SLT_beta] (6)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (STXB_BPH30 | P69178)
biological process
    GO:0019836    hemolysis by symbiont of host erythrocytes    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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,B,C,D,E   (STXB_BPH19 | P69179)
biological process
    GO:0019836    hemolysis by symbiont of host erythrocytes    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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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  2xsc
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  STXB_BPH30 | P69178
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 Related Entries

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

UniProtKB/Swiss-Prot
        STXB_BPH19 | P69179: 1bos 1c48 1c4q 1cqf 1czg 1czw 1d1i 1d1k 1ojf 1qnu 2c5c 4ull
        STXB_BPH30 | P69178: 1bos 1c48 1c4q 1cqf 1czg 1czw 1d1i 1d1k 1ojf 2c5c 4ull

(-) Related Entries Specified in the PDB File

1ojf PENTAMERIC SINGLE DOMAIN ANTIBODY 1V5