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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SSL3-TLR2 COMPLEX
 
Authors :  L. J. Feitsma, E. G. Huizinga
Date :  06 Aug 15  (Deposition) - 19 Aug 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Superantigens, Superantigen-Like Proteins, Ssl, Ssl3, Toll-Like Receptor 2, Tlr2, Tlr6, Immunology, Inflammation, Inhibition, Lipopeptide, Phosphatidylcholine, Pc, Immune Evasion, Innate Immunity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Koymans, L. J. Feitsma, T. H. Brondijk, P. C. Aerts, E. Lukkien, P. Lossl, K. P. Van Kessel, C. J. De Haas, J. A. Van Strijp, E. G. Huizinga
Structural Basis For Inhibition Of Tlr2 By Staphylococcal Superantigen-Like Protein 3 (Ssl3).
Proc. Natl. Acad. Sci. Usa V. 112 11018 2015
PubMed-ID: 26283364  |  Reference-DOI: 10.1073/PNAS.1502026112

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 2
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293-EBNA1-S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 25-589
    Gene: TLR2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN 3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA-GAMI
    Gene: SAOUHSC_00386
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325)
    Organism Taxid: 93061

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCW1Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:266 , ILE A:314 , PHE A:322 , SER A:346 , LYS A:347 , PHE A:349 , PRO A:352 , PHE A:355 , CL A:805 , LEU B:160 , LYS B:161binding site for residue PCW A 804
2AC2SOFTWAREPCW A:804binding site for residue CL A 805
3AC3SOFTWAREPRO A:387 , LYS A:413 , ASN A:414binding site for Mono-Saccharide NAG A 801 bound to ASN A 414
4AC4SOFTWARESER A:395 , SER A:421 , ARG A:422 , PHE A:440 , ASN A:442 , ASP A:463binding site for Poly-Saccharide residues NAG A 802 through NAG A 803 bound to ASN A 442

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:36
2A:353 -A:382
3A:432 -A:454
4A:537 -A:564

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:558 -Pro A:559
2Ser A:566 -Pro A:567
3Gly B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D3I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D3I)

(-) Exons   (0, 0)

(no "Exon" information available for 5D3I)

(-) 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:549
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eee..................eee.......ee............eee.......ee............eee.....................eee......................eeeeee.....ee.........eeeeeeeee....ee.........eeeeeeee.....hhhhhhhhhh....eeeee......................eeeee..eehhhhhhhhhhhhhhh....eeeee..ee.....................eeeee............hhhhhhhh....eeeee.......hhhhhhhh....eee......hhhhhhhhh.........eee.......hhhhhhhhhhhh....eee....................eee..................eee.................eee..........hhhhh....eee.........hhhhhhhh....eee.....ee.hhhhhhhhhhhhhhhhh.........eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d3i A  27 SLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTLHLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSSTGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMKIRENAVSTFSKDQLGSFPKLETLEAGDNHFVCSCELLSFTMETPALAQILVDWPDSYLCDSPPRLHGHRL 575
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566         


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeeeee..........eeee......eeee..hhhhhhh....eeeeeeee...........eee..eee.......eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhhh......eeeeeeee....eeeee.....hhhhhh.eee...eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d3i B 137 KYEDLRAYYTKPSFEFEKQFGFMLKPWTTVRFMNVIPNRFIYKIALVGKDEKKYKDGPYDNIDVFIVLEDNKYQLKKYSVGGITKTNSKKVNHKVELSITKKDNQGMISRDVSEYMITKEEISLKELDFKLRKQLIEKHNLYGNMGSGTIVIKMKNGGKYTFELHKKLQEHRMADVIDGTNIDNIEVNIK 326
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
   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  (0, 0)

(no "SCOP Domain" information available for 5D3I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D3I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D3I)

(-) Gene Ontology  (80, 80)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:193 - Pro B:194   [ RasMol ]  
    Ser A:566 - Pro A:567   [ RasMol ]  
    Trp A:558 - Pro A:559   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        TLR2_MOUSE | Q9QUN7: 2z81 2z82 3a79 3a7b 3a7c
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(-) Related Entries Specified in the PDB File

5d3d 5D3D CONTAINS UNBOUND STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN 3 (SSL3)