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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHOLERA TOXIN-LIKE B-SUBUNIT FROM CITROBACTER FREUNDII TO 1.9 ANGSTROM
 
Authors :  L. Jansson, M. Lebens, A. Imberty, A. Varrot, S. Teneberg
Date :  15 Oct 09  (Deposition) - 27 Oct 09  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  D,E,F,G,H,I,J,K,L,M
Biol. Unit 1:  I,J,K,L,M  (1x)
Biol. Unit 2:  D,E,F,G,H  (1x)
Keywords :  Lectin, B Subunit, Cholera Toxin-Like, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Jansson, J. Angstrom, M. Lebens, A. Imberty, A. Varrot, S. Teneberg
Carbohydrate Binding Specificities And Crystal Structure Of The Cholera Toxin-Like B-Subunit From Citrobacter Freundii.
Biochimie V. 92 482 2010
PubMed-ID: 20171259  |  Reference-DOI: 10.1016/J.BIOCHI.2010.02.010

(-) Compounds

Molecule 1 - CFXB
    Chains: D, E, F, G, H, I, J, K, L, M
    Engineered: YES
    Expression System: VIBRIO CHOLERAE
    Expression System Plasmid: PML-HCFXBTAC
    Expression System Strain: JS1569
    Expression System Taxid: 666
    Expression System Vector: PML
    Fragment: B SUBUNIT, RESIDUES 23-125
    Organism Scientific: CITROBACTER FREUNDII
    Organism Taxid: 546
    Synonym: AB5 TOXIN

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : DEFGHIJKLM
Biological Unit 1 (1x):      IJKLM
Biological Unit 2 (1x): DEFGH     

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL8Ligand/IonGLYCEROL
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL3Ligand/IonGLYCEROL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA J:46 , THR J:47 , ASN J:94BINDING SITE FOR RESIDUE EDO J1103
02AC2SOFTWARETYR L:76 , PHE L:77BINDING SITE FOR RESIDUE EDO L1103
03AC3SOFTWAREALA D:46 , THR D:47 , PRO D:93 , ASN D:94BINDING SITE FOR RESIDUE EDO D1104
04AC4SOFTWAREALA E:74 , HOH E:2043BINDING SITE FOR RESIDUE GOL E1103
05AC5SOFTWARETYR E:18 , GLY E:45 , ALA E:46 , THR E:47 , PRO E:93 , ASN E:94BINDING SITE FOR RESIDUE GOL E1104
06AC6SOFTWAREALA F:74 , ALA G:74BINDING SITE FOR RESIDUE GOL G1104
07AC7SOFTWARETYR I:18 , ALA I:46 , THR I:47 , PRO I:93 , ASN I:94BINDING SITE FOR RESIDUE GOL I1103
08AC8SOFTWAREALA I:74 , ALA J:74 , HOH J:2033BINDING SITE FOR RESIDUE GOL I1104
09AC9SOFTWAREALA J:74 , ALA K:74 , HOH K:2033BINDING SITE FOR RESIDUE GOL K1103
10BC1SOFTWAREGOL M:1104BINDING SITE FOR RESIDUE GOL L1104
11BC2SOFTWAREGOL L:1104 , ARG M:73BINDING SITE FOR RESIDUE GOL M1104

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1D:9 -D:86
2E:9 -E:86
3F:9 -F:86
4G:9 -G:86
5H:9 -H:86
6I:9 -I:86
7J:9 -J:86
8K:9 -K:86
9L:9 -L:86
10M:9 -M:86

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Thr D:92 -Pro D:93
2Thr E:92 -Pro E:93
3Thr F:92 -Pro F:93
4Thr G:92 -Pro G:93
5Thr H:92 -Pro H:93
6Thr I:92 -Pro I:93
7Thr J:92 -Pro J:93
8Thr K:92 -Pro K:93
9Thr L:92 -Pro L:93
10Thr M:92 -Pro M:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WV6)

(-) Exons   (0, 0)

(no "Exon" information available for 2WV6)

(-) Sequences/Alignments

Asymmetric 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 D from PDB  Type:PROTEIN  Length:92
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    32        42        52        62        72        82        92       102       112       122   
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 125
               SCOP domains d2wv6d_ D: automated matches                                                                            SCOP domains
               CATH domains 2wv6D00 D:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee....eeeeee.....eee....-----------hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2wv6 D   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVP-----------LERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 103
                                    10        20        30        40        50  |      -    |   70        80        90       100   
                                                                               53          65                                      


Chain E from PDB  Type:PROTEIN  Length:89
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:102
                                    32        42        52        62        72        82        92       102       112       122  
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 124
               SCOP domains d2wv6e_ E: automated matches                                                                           SCOP domains
               CATH domains 2wv6E00 E:1-102  [code=2.40.50.11   0, no name defi          ned]                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee..---eeeee.....eee..----------.hhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2wv6 E   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAG---MVIISFANGATFQVE----------KRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 102
                                    10        20        30  |   | 40        50|        - |      70        80        90       100  
                                                           33  37            51         62                                        


Chain F from PDB  Type:PROTEIN  Length:93
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    32        42        52        62        72        82        92       102       112       122   
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 125
               SCOP domains d2wv6f_ F: automated matches                                                                            SCOP domains
               CATH domains 2wv6F00 F:1-103  [code=2.40.50.1    10, no name def      ined]                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee.----eeeee.....eee..------.....hhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2wv6 F   1 APQNITELCSEYHNTQIYELNKEIKTYTESLA----MVIISFANGATFQVE------LESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 103
                                    10        20        30 |    | 40        50|      |60        70        80        90       100   
                                                          32   37            51     58                                             


Chain G from PDB  Type:PROTEIN  Length:102
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    32        42        52        62        72        82        92       102       112       122   
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 125
               SCOP domains d2wv6g_ G: automated matches                                                                            SCOP domains
               CATH domains 2wv6G00 G:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee....eeeeee.....eee........-......hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2wv6 G   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQH-ESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 103
                                    10        20        30        40        50      | 60        70        80        90       100   
                                                                                   57 |                                            
                                                                                     59                                            


Chain H from PDB  Type:PROTEIN  Length:94
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    32        42        52        62        72        82        92       102       112       122   
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 125
               SCOP domains d2wv6h_ H: automated matches                                                                            SCOP domains
               CATH domains 2wv6H00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee....eeeeee.....eee...---------.hhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2wv6 H   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEV---------KRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 103
                                    10        20        30        40        50 |       - |      70        80        90       100   
                                                                              52        62                                         


Chain I from PDB  Type:PROTEIN  Length:92
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:102
                                    32        42        52        62        72        82        92       102       112       122  
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 124
               SCOP domains d2wv6i_ I: automated matches                                                                           SCOP domains
               CATH domains 2wv6I00 I:1-102  [code=2.40.50.110, no name defined          ]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeee.......eeee.....eeee.----------.hhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2wv6 I   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVE----------KRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 102
                                    10        20        30        40        50|        - |      70        80        90       100  
                                                                             51         62                                        


Chain J from PDB  Type:PROTEIN  Length:99
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:102
                                    32        42        52        62        72        82        92       102       112       122  
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 124
               SCOP domains d2wv6j_ J: automated matches                                                                           SCOP domains
               CATH domains 2wv6J00 J:1-102  [code=2.40.50.1   10, no name defined]                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee.---eeeeee.....eee.............hhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2wv6 J   1 APQNITELCSEYHNTQIYELNKEIKTYTESLA---EMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 102
                                    10        20        30 |   |  40        50        60        70        80        90       100  
                                                          32  36                                                                  


Chain K from PDB  Type:PROTEIN  Length:94
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:102
                                    32        42        52        62        72        82        92       102       112       122  
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 124
               SCOP domains d2wv6k_ K: automated matches                                                                           SCOP domains
               CATH domains 2wv6K00 K:1-102  [code=2.40.50.110, no name defined]                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee....eeeeee.....eee....--------.hhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2wv6 K   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVP--------KRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 102
                                    10        20        30        40        50  |      - |      70        80        90       100  
                                                                               53       62                                        


Chain L from PDB  Type:PROTEIN  Length:91
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:102
                                    32        42        52        62        72        82        92       102       112       122  
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 124
               SCOP domains d2wv6l_ L: automated matches                                                                           SCOP domains
               CATH domains 2wv6L00 L:1-102  [code=2.40.50.11  0, no name defin         ed]                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee..--eeeeee.....eee..---------....hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2wv6 L   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAG--EMVIISFANGATFQVE---------QKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELS 102
                                    10        20        30  |  |  40        50|        -|       70        80        90       100  
                                                           33 36             51        61                                         


Chain M from PDB  Type:PROTEIN  Length:92
 aligned with Q8GAV5_CITFR | Q8GAV5 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    32        42        52        62        72        82        92       102       112       122   
         Q8GAV5_CITFR    23 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 125
               SCOP domains d2wv6m_ M: automated matches                                                                            SCOP domains
               CATH domains 2wv6M00 M:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...eeeeeeeee..eeeeee....eeeeee.....eee...-----------.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2wv6 M   1 APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEV-----------PLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIELSN 103
                                    10        20        30        40        50 |       -   |    70        80        90       100   
                                                                              52          64
   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, 10)

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

(-) CATH Domains  (1, 10)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WV6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain D,E,F,G,H,I,J,K,L,M   (Q8GAV5_CITFR | Q8GAV5)
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.
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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  2wv6
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  Q8GAV5_CITFR | Q8GAV5
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    Protein Cavities: castP
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
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  Q8GAV5_CITFR | Q8GAV5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2WV6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WV6)