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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN 11
 
Authors :  M. C. Chung, B. D. Wines, H. Baker, R. J. Langley, E. N. Baker, J. D. Fraser
Date :  24 Sep 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ob Fold, Beta Grasp, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Chung, B. D. Wines, H. Baker, R. J. Langley, E. N. Baker, J. D. Frase
The Crystal Structure Of Staphylococcal Superantigen-Like Protein 11 In Complex With Sialyl Lewis X Reveals The Mechanism For Cell Binding And Immune Inhibition
Mol. Microbiol. V. 66 1342 2007
PubMed-ID: 18045383  |  Reference-DOI: 10.1111/J.1365-2958.2007.05989.X

(-) Compounds

Molecule 1 - SUPERANTIGEN-LIKE PROTEIN 11
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A-3C
    Expression System Strain: AD494
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSL11
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: US6610

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2RDH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RDH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:75 -Arg B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RDH)

(-) 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 A from PDB  Type:PROTEIN  Length:185
 aligned with A8E1U5_STAAU | A8E1U5 from UniProtKB/TrEMBL  Length:196

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
         A8E1U5_STAAU     6 RSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
               SCOP domains d2rdha1 A:6-93 automated matches                                                        d2rdha2 A:94-196 automated matches                                                                      SCOP domains
               CATH domains 2rdhA01      2rdhA02 A:19-89  [code=2.40.50.110, no name defined]                   2rdhA01 A:6-18,A:90-196  [code=3.10.20.120, no name defined]                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeeeeeeeee..eeeeee..eeeeee...hhhhhh..eeeeeeeeee...------.eeee..eee..........eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhh..........eeeeee....eeeee.....hhhhh..eee...eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rdh A   6 RSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVRE------DNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
                                    15        25        35        45        55        65      |  -   |    85        95       105       115       125       135       145       155       165       175       185       195 
                                                                                             72     79                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with A8E1U5_STAAU | A8E1U5 from UniProtKB/TrEMBL  Length:196

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
         A8E1U5_STAAU     6 RSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
               SCOP domains d2rdhb1 B:6-93 automated matches                                                        d2 rdhb2 B:94-196 automated matches                                                                     SCOP domains
               CATH domains 2rdhB01      2rdhB02 B:19-89  [code=2.40.50.110, no name defined]                   2rdhB0 1 B:6-18,B:90-196  [code=3.10.20.120, no name defined]                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeeeeeeeee..eeeee....eeeee...hhhhhh..eeeeeeeeee..........eeee..eee.......-..eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh..eee...eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rdh B   6 RSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHI-TVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
                                    15        25        35        45        55        65        75        85        95 |     105       115       125       135       145       155       165       175       185       195 
                                                                                                                    95 |                                                                                                   
                                                                                                                      97                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:192
 aligned with A8E1U5_STAAU | A8E1U5 from UniProtKB/TrEMBL  Length:196

    Alignment length:192
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  
         A8E1U5_STAAU     5 VRSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
               SCOP domains d2rdhc1 C:5-93 automated matches                                                         d2rdhc2 C:94-196 automated matches                                                                      SCOP domains
               CATH domains 2rdhC01       2rdhC02 C:19-89  [code=2.40.50.110, no name defined]                   2rdhC01 C:5-18,C:90-196  [code=3.10.20.120, no name defined]                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeeeeeeeee..eeeee....eeeee...hhhhhh..eeeeeeeeee..........eeee..eee..........eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh..eee...eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rdh C   5 VRSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  


Chain D from PDB  Type:PROTEIN  Length:191
 aligned with A8E1U5_STAAU | A8E1U5 from UniProtKB/TrEMBL  Length:196

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
         A8E1U5_STAAU     6 RSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
               SCOP domains d2rdhd1 D:6-93 automated matches                                                        d2rdhd2 D:94-196 automated matches                                                                      SCOP domains
               CATH domains 2rdhD01      2rdhD02 D:19-89  [code=2.40.50.110, no name defined]                   2rdhD01 D:6-18,D:90-196  [code=3.10.20.120, no name defined]                                                CATH domains
           Pfam domains (1) -----DUF1954-2rdhD05 D:11-90                                                         --------Stap_Strp_tox_C-2rdhD01 D:99-196                                                                   Pfam domains (1)
           Pfam domains (2) -----DUF1954-2rdhD06 D:11-90                                                         --------Stap_Strp_tox_C-2rdhD02 D:99-196                                                                   Pfam domains (2)
           Pfam domains (3) -----DUF1954-2rdhD07 D:11-90                                                         --------Stap_Strp_tox_C-2rdhD03 D:99-196                                                                   Pfam domains (3)
           Pfam domains (4) -----DUF1954-2rdhD08 D:11-90                                                         --------Stap_Strp_tox_C-2rdhD04 D:99-196                                                                   Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhh...eeeeeeeeeee..eeeeee..eeeeee...hhhhhh..eeeeeeeeee.......hhhhhee..eee..........eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhh..........eeeeee....eeeee.....hhhhh..eee...eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rdh D   6 RSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
   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  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: Ant-toxin_C (48)
(-)
Clan: no clan defined [family: DUF1954] (9)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A8E1U5_STAAU | A8E1U5)
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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 Related Entries

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

UniProtKB/TrEMBL
        A8E1U5_STAAU | A8E1U5: 2rdg

(-) Related Entries Specified in the PDB File

2rdg THE SAME PROTEIN COMPLEXED WITH SIALYL LEWIS X