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(-) Description

Title :  THE COMPLEX OF THE MUTATED SHIGA TOXIN B SUBUNIT AND GB3 TRISACCHARIDE
 
Authors :  H. Ling, D. Bast, J. L. Brunton, R. J. Read
Date :  06 Aug 99  (Deposition) - 07 Aug 00  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Bacterial Toxin, Sugar Receptor Binding Domain, Protein- Carbohydrate Recognition, Ob-Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ling, D. Bast, J. L. Brunton, R. J. Read
The Complex Of The Mutated Shiga Toxin B Subunit And Gb3 Trisaccharide
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHIGA TOXIN B-CHAIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SHIGA-LIKE TOXIN I BINDING DOMAIN
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: COMPLEXED WITH TRISACCHARIDE OF GLYCOLIPID GB3

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2GAL6Ligand/IonBETA-D-GALACTOSE
3GLA6Ligand/IonALPHA D-GALACTOSE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:132 , ARG A:133 , TRP A:134 , ASN A:135 , GAL A:181 , HOH A:672 , ASP B:218 , TRP B:234BINDING SITE FOR RESIDUE GLA A 180
02AC2SOFTWARETRP A:134 , GLA A:180 , BGC A:182 , HOH A:672BINDING SITE FOR RESIDUE GAL A 181
03AC3SOFTWAREGAL A:181 , HOH A:703BINDING SITE FOR RESIDUE BGC A 182
04AC4SOFTWAREASN B:232 , ARG B:233 , TRP B:234 , ASN B:235 , GAL B:281 , ASP C:318 , TRP C:334 , LYS E:508BINDING SITE FOR RESIDUE GLA B 280
05AC5SOFTWARETRP B:234 , GLA B:280 , BGC B:282 , BGC C:382BINDING SITE FOR RESIDUE GAL B 281
06AC6SOFTWAREGAL B:281 , BGC C:382BINDING SITE FOR RESIDUE BGC B 282
07AC7SOFTWARELYS B:213 , ASN B:215 , THR B:221 , GLU B:228 , PHE B:230 , GLY B:260 , GAL B:271 , HOH B:610 , HOH B:639BINDING SITE FOR RESIDUE GLA B 270
08AC8SOFTWAREASP B:217 , THR B:219 , PHE B:230 , GLY B:260 , GLA B:270 , BGC B:272 , HOH B:610BINDING SITE FOR RESIDUE GAL B 271
09AC9SOFTWARELYS B:253 , GAL B:271 , HOH B:610 , HOH B:615 , HOH B:659BINDING SITE FOR RESIDUE BGC B 272
10BC1SOFTWAREARG C:333 , TRP C:334 , ASN C:335 , GAL C:381 , HOH C:690 , TYR D:414 , ASP D:418BINDING SITE FOR RESIDUE GLA C 380
11BC2SOFTWARETRP C:334 , GLA C:380 , BGC C:382 , HOH C:635 , HOH C:662 , HOH C:690BINDING SITE FOR RESIDUE GAL C 381
12BC3SOFTWAREGAL B:281 , BGC B:282 , GAL C:381 , BGC D:482 , THR E:546BINDING SITE FOR RESIDUE BGC C 382
13BC4SOFTWAREASN D:432 , ARG D:433 , TRP D:434 , ASN D:435 , GAL D:481 , TYR E:514 , ASP E:518 , TRP E:534BINDING SITE FOR RESIDUE GLA D 480
14BC5SOFTWARELYS A:108 , TRP D:434 , GLA D:480 , BGC D:482BINDING SITE FOR RESIDUE GAL D 481
15BC6SOFTWARETHR A:146 , BGC C:382 , GAL D:481 , HOH D:683BINDING SITE FOR RESIDUE BGC D 482
16BC7SOFTWARETYR A:114 , ASP A:118 , ASN E:532 , ARG E:533 , TRP E:534 , ASN E:535 , GAL E:581BINDING SITE FOR RESIDUE GLA E 580
17BC8SOFTWARETRP E:534 , GLA E:580 , BGC E:582BINDING SITE FOR RESIDUE GAL E 581
18BC9SOFTWAREHOH A:703 , GAL E:581 , HOH E:700BINDING SITE FOR RESIDUE BGC E 582

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:104 -A:157
2B:204 -B:257
3C:304 -C:357
4D:404 -D:457
5E:504 -E:557

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CQF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CQF)

(-) 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 d1cqfa_ A: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfA00 A:101-169  [code=2.40.50.70, no name defined]                 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
                 1cqf A 101 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 169
                                   110       120       130       140       150       160         


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 d1cqfa_ A: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfA00 A:101-169  [code=2.40.50.70, no name defined]                 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
                 1cqf A 101 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 169
                                   110       120       130       140       150       160         


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 d1cqfb_ B: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfB00 B:201-269  [code=2.40.50.70, no name defined]                 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
                 1cqf B 201 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 269
                                   210       220       230       240       250       260         


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 d1cqfb_ B: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfB00 B:201-269  [code=2.40.50.70, no name defined]                 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
                 1cqf B 201 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 269
                                   210       220       230       240       250       260         


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 d1cqfc_ C: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfC00 C:301-369  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1cqf C 301 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 369
                                   310       320       330       340       350       360         


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 d1cqfc_ C: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfC00 C:301-369  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1cqf C 301 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 369
                                   310       320       330       340       350       360         


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 d1cqfd_ D: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfD00 D:401-469  [code=2.40.50.70, no name defined]                 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
                 1cqf D 401 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 469
                                   410       420       430       440       450       460         


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 d1cqfd_ D: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfD00 D:401-469  [code=2.40.50.70, no name defined]                 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
                 1cqf D 401 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 469
                                   410       420       430       440       450       460         


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 d1cqfe_ E: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfE00 E:501-569  [code=2.40.50.70, no name defined]                 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
                 1cqf E 501 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 569
                                   510       520       530       540       550       560         


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 d1cqfe_ E: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1cqfE00 E:501-569  [code=2.40.50.70, no name defined]                 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
                 1cqf E 501 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGTFSEVIFR 569
                                   510       520       530       540       550       560
   Legend:   → Mismatch (orange background)
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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  (1, 5)

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

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CQF)

(-) 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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  STXB_BPH19 | P69179
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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 1czg 1czw 1d1i 1d1k 1ojf 1qnu 2c5c 2xsc 4ull
        STXB_BPH30 | P69178: 1bos 1c48 1c4q 1czg 1czw 1d1i 1d1k 1ojf 2c5c 2xsc 4ull

(-) Related Entries Specified in the PDB File

1bos 1BOS CONTAINS THE WILDTYPE PROTEIN IN COMPLEXED WITH THE GB3 TRISACCHARIDE.