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(-) Description

Title :  CRYSTAL STRUCTURE OF THE B-SUBUNIT OF THE AB5 TOXIN FROM E. COLI
 
Authors :  E. Byres, A. W. Paton, J. C. Paton, J. C. Lofling, D. F. Smith, M. C. J. Wilce, U. M. Talbot, D. C. Chong, H. Yu, S. Huang, X. Chen, N. M. Varki, A. Varki, J. Rossjohn, T. Beddoe
Date :  22 Jul 08  (Deposition) - 04 Nov 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Byres, A. W. Paton, J. C. Paton, J. C. Lofling, D. F. Smith, M. C. J. Wilce, U. M. Talbot, D. C. Chong, H. Yu, S. Huang, X. Chen, N. M. Varki, A. Varki, J. Rossjohn, T. Beddoe
Incorporation Of A Non-Human Glycan Mediates Human Susceptibility To A Bacterial Toxin
Nature V. 456 648 2008
PubMed-ID: 18971931  |  Reference-DOI: 10.1038/NATURE07428
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUBTILASE CYTOTOXIN, SUBUNIT B
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES IN DATABASE 24-141
    Gene: SUBB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: SUBB

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
11PE5Ligand/IonPENTAETHYLENE GLYCOL
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:62 , TYR A:66 , THR A:69 , 1PE C:127BINDING SITE FOR RESIDUE 1PE A 127
2AC2SOFTWAREASN B:62 , TYR B:66 , HOH B:177 , THR E:69 , 1PE E:127BINDING SITE FOR RESIDUE 1PE B 127
3AC3SOFTWARE1PE A:127 , HOH C:204 , THR D:69BINDING SITE FOR RESIDUE 1PE C 127
4AC4SOFTWARETYR D:66 , THR D:70BINDING SITE FOR RESIDUE 1PE D 127
5AC5SOFTWARE1PE B:127 , ASN E:62BINDING SITE FOR RESIDUE 1PE E 127

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:45
2A:103 -A:109
3B:31 -B:45
4B:103 -B:109
5C:31 -C:45
6C:103 -C:109
7D:31 -D:45
8D:103 -D:109
9E:31 -E:45
10E:103 -E:109

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Asp A:8 -Gly A:9
2Asp B:8 -Gly B:9
3Ser B:37 -Ala B:38
4Asp C:8 -Gly C:9
5Asp D:8 -Gly D:9
6Asp E:8 -Gly E:9
7Gln E:36 -Ser E:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DWA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DWA)

(-) Exons   (0, 0)

(no "Exon" information available for 3DWA)

(-) 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:118
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:118
                                    33        43        53        63        73        83        93       103       113       123       133        
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKNS 141
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwa A   1 EWTGDARDGmFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSmKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKNS 118
                                    10        20        30        40      | 50        60        70        80        90       100       110        
                                    10-MSE                               47-MSE                                                                   


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:117
                                    33        43        53        63        73        83        93       103       113       123       133       
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 140
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwa B   1 EWTGDARDGmFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSmKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 117
                                    10        20        30        40      | 50        60        70        80        90       100       110       
                                    10-MSE                               47-MSE                                                                  


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:120
                                                                                                                                               141  
                                    33        43        53        63        73        83        93       103       113       123       133       | -
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKNS--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dwa C   1 EWTGDARDGmFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSmKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKNSLE 120
                                    10        20        30        40      | 50        60        70        80        90       100       110       120
                                    10-MSE                               47-MSE                                                                     


Chain D from PDB  Type:PROTEIN  Length:117
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:117
                                    33        43        53        63        73        83        93       103       113       123       133       
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 140
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwa D   1 EWTGDARDGmFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSmKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 117
                                    10        20        30        40      | 50        60        70        80        90       100       110       
                                    10-MSE                               47-MSE                                                                  


Chain E from PDB  Type:PROTEIN  Length:116
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:116
                                    33        43        53        63        73        83        93       103       113       123       133      
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKK 139
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwa E   1 EWTGDARDGmFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSmKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKK 116
                                    10        20        30        40      | 50        60        70        80        90       100       110      
                                    10-MSE                               47-MSE
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 3DWA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DWA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DWA)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q3ZTX8_ECOLX | Q3ZTX8)
biological process
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q3ZTX8_ECOLX | Q3ZTX8: 3dwp 3dwq 4bwg

(-) Related Entries Specified in the PDB File

3dwp 3dwq