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(-) Description

Title :  A MUTANT SHIGA-LIKE TOXIN IIE BOUND TO ITS RECEPTOR
 
Authors :  H. Ling, A. Boodhoo, G. D. Armstrong, C. G. Clark, J. L. Brunton, R. J. Read
Date :  20 Oct 98  (Deposition) - 20 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Toxin, Receptor Binding, Protein-Carbohydrate Recognition, Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ling, N. S. Pannu, A. Boodhoo, G. D. Armstrong, C. G. Clark, J. L. Brunton, R. J. Read
A Mutant Shiga-Like Toxin Iie Bound To Its Receptor Gb(3): Structure Of A Group Ii Shiga-Like Toxin With Altered Binding Specificity.
Structure Fold. Des. V. 8 253 2000
PubMed-ID: 10745005  |  Reference-DOI: 10.1016/S0969-2126(00)00103-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RECEPTOR-BINDING DOMAIN
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: COMPLEXED WITH PK-MCO, AN ANALOGUE OF GB3 (GLOBOTRIAOSYL CERAMIDE)
    Synonym: VEROCYTOTOXIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1GAL7Ligand/IonBETA-D-GALACTOSE
2GLA7Ligand/IonALPHA D-GALACTOSE
3GLC5Ligand/IonALPHA-D-GLUCOSE
4NBU3Ligand/IonN-BUTANE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:130 , THR A:131 , ASN A:132 , ARG A:133 , PHE A:163 , GAL A:191 , HOH A:195 , HOH A:196BINDING SITE FOR RESIDUE GLA A 190
02AC2SOFTWARESER A:154 , ASN A:155 , GLY A:162 , GLA A:190 , GLC A:192 , HOH A:194 , HOH A:195 , HOH A:197 , HOH A:209 , HOH A:219BINDING SITE FOR RESIDUE GAL A 191
03AC3SOFTWAREASN A:155 , GAL A:191 , NBU A:193 , GLC C:392 , THR E:546BINDING SITE FOR RESIDUE GLC A 192
04AC4SOFTWAREHOH B:51 , HOH B:129 , TRP B:230 , THR B:231 , ASN B:232 , ARG B:233 , PHE B:263 , GAL B:291 , GLU C:316BINDING SITE FOR RESIDUE GLA B 290
05AC5SOFTWAREHOH B:51 , HOH B:88 , HOH B:116 , HOH B:123 , SER B:254 , ASN B:255 , GLY B:262 , GLA B:290 , GLC B:292 , GLU C:316BINDING SITE FOR RESIDUE GAL B 291
06AC6SOFTWAREASN B:255 , GAL B:291 , ASN D:435 , TRP E:534BINDING SITE FOR RESIDUE GLC B 292
07AC7SOFTWAREHOH C:72 , HOH C:74 , HOH C:120 , TRP C:330 , THR C:331 , ASN C:332 , ARG C:333 , PHE C:363 , ALA C:364 , GAL C:391BINDING SITE FOR RESIDUE GLA C 390
08AC8SOFTWAREHOH C:73 , HOH C:74 , HOH C:79 , SER C:354 , ASN C:355 , GLY C:362 , GLA C:390 , GLC C:392 , HOH D:160BINDING SITE FOR RESIDUE GAL C 391
09AC9SOFTWAREGLC A:192 , THR B:246 , ASN C:355 , GAL C:391 , NBU C:393BINDING SITE FOR RESIDUE GLC C 392
10BC1SOFTWAREGLU A:116 , HOH E:52 , HOH E:109 , TRP E:530 , THR E:531 , ASN E:532 , ARG E:533 , PHE E:563 , GAL E:591BINDING SITE FOR RESIDUE GLA E 590
11BC2SOFTWAREHOH E:53 , HOH E:108 , HOH E:109 , SER E:554 , ASN E:555 , GLY E:562 , GLA E:590 , GLC E:592BINDING SITE FOR RESIDUE GAL E 591
12BC3SOFTWAREHOH E:89 , ASN E:555 , GAL E:591 , NBU E:593BINDING SITE FOR RESIDUE GLC E 592
13BC4SOFTWARELYS A:113 , ASN A:115 , THR A:121 , GLU A:128 , TRP A:130 , GAL A:171 , HOH A:199BINDING SITE FOR RESIDUE GLA A 170
14BC5SOFTWAREASP A:117 , TRP A:130 , GLY A:160 , GLA A:170 , GLC A:172BINDING SITE FOR RESIDUE GAL A 171
15BC6SOFTWAREGAL A:171BINDING SITE FOR RESIDUE GLC A 172
16BC7SOFTWAREHOH B:128 , LYS B:213 , ASN B:215 , THR B:221 , GLU B:228 , TRP B:230 , GAL B:271BINDING SITE FOR RESIDUE GLA B 270
17BC8SOFTWAREASP B:217 , THR B:219 , TRP B:230 , GLY B:260 , GLA B:270BINDING SITE FOR RESIDUE GAL B 271
18BC9SOFTWAREHOH E:86 , LYS E:513 , ASN E:515 , THR E:521 , GLU E:528 , TRP E:530 , GAL E:571BINDING SITE FOR RESIDUE GLA E 570
19CC1SOFTWAREASP E:517 , THR E:519 , TRP E:530 , GLY E:560 , GLA E:570BINDING SITE FOR RESIDUE GAL E 571
20CC2SOFTWARELEU A:145 , GLC A:192BINDING SITE FOR RESIDUE NBU A 193
21CC3SOFTWAREGLC C:392BINDING SITE FOR RESIDUE NBU C 393
22CC4SOFTWAREASP B:203 , CYS B:204 , GLC E:592BINDING SITE FOR RESIDUE NBU E 593

(-) 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 2BOS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BOS)

(-) 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:68
 aligned with Q47644_ECOLX | Q47644 from UniProtKB/TrEMBL  Length:87

    Alignment length:68
                                    29        39        49        59        69        79        
         Q47644_ECOLX    20 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  87
               SCOP domains d2bosa_ A: Verotoxin-1/shiga-toxin, B-pentamer                       SCOP domains
               CATH domains 2bosA00 A:102-169  [code=2.40.50.70, no name defined]                CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bos A 102 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAEVQFN 169
                                   111       121       131       141       151       161        


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with Q47644_ECOLX | Q47644 from UniProtKB/TrEMBL  Length:87

    Alignment length:68
                                    29        39        49        59        69        79        
         Q47644_ECOLX    20 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  87
               SCOP domains d2bosb_ B: Verotoxin-1/shiga-toxin, B-pentamer                       SCOP domains
               CATH domains 2bosB00 B:202-269  [code=2.40.50.70, no name defined]                CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bos B 202 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAEVQFN 269
                                   211       221       231       241       251       261        


Chain C from PDB  Type:PROTEIN  Length:68
 aligned with Q47644_ECOLX | Q47644 from UniProtKB/TrEMBL  Length:87

    Alignment length:68
                                    29        39        49        59        69        79        
         Q47644_ECOLX    20 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  87
               SCOP domains d2bosc_ C: Verotoxin-1/shiga-toxin, B-pentamer                       SCOP domains
               CATH domains 2bosC00 C:302-369  [code=2.40.50.70, no name defined]                CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bos C 302 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAEVQFN 369
                                   311       321       331       341       351       361        


Chain D from PDB  Type:PROTEIN  Length:68
 aligned with Q47644_ECOLX | Q47644 from UniProtKB/TrEMBL  Length:87

    Alignment length:68
                                    29        39        49        59        69        79        
         Q47644_ECOLX    20 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  87
               SCOP domains d2bosd_ D: Verotoxin-1/shiga-toxin, B-pentamer                       SCOP domains
               CATH domains 2bosD00 D:402-469  [code=2.40.50.70, no name defined]                CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bos D 402 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAEVQFN 469
                                   411       421       431       441       451       461        


Chain E from PDB  Type:PROTEIN  Length:68
 aligned with Q47644_ECOLX | Q47644 from UniProtKB/TrEMBL  Length:87

    Alignment length:68
                                    29        39        49        59        69        79        
         Q47644_ECOLX    20 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  87
               SCOP domains d2bose_ E: Verotoxin-1/shiga-toxin, B-pentamer                       SCOP domains
               CATH domains 2bosE00 E:502-569  [code=2.40.50.70, no name defined]                CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bos E 502 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAEVQFN 569
                                   511       521       531       541       551       561
   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  (1, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BOS)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q47644_ECOLX | Q47644)
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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        Q47644_ECOLX | Q47644: 1qoh 4p2c

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