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(-) Description

Title :  CRYSTAL STRUCTURE AT 2.7A RESOLUTION OF A COMPLEX BETWEEN A STAPHYLOCOCCUS AUREUS DOMAIN AND A FAB FRAGMENT OF A HUMAN IGM ANTIBODY
 
Authors :  M. Graille, E. A. Stura, A. L. Corper, B. J. Sutton, M. J. Taussig, J. B. Charbonnier, G. J. Silverman
Date :  15 Nov 99  (Deposition) - 24 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D,G  (1x)
Biol. Unit 3:  E,F,H  (1x)
Biol. Unit 4:  E,F  (1x)
Biol. Unit 5:  C,D  (1x)
Keywords :  Fab-Ibp Complex Crystal Structure 2. 7A Resolution Binding Outside The Antigen Combining Site Superantigen Fab Vh3 Specificity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Graille, E. A. Stura, A. L. Corper, B. J. Sutton, M. J. Taussig, J. B. Charbonnier, G. J. Silverman
Crystal Structure Of A Staphylococcus Aureus Protein A Domain Complexed With The Fab Fragment Of A Human Igm Antibody: Structural Basis For Recognition Of B-Cell Receptors And Superantigen Activity.
Proc. Natl. Acad. Sci. Usa V. 97 5399 2000
PubMed-ID: 10805799  |  Reference-DOI: 10.1073/PNAS.97.10.5399
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGM RF 2A2
    Chains: A, C, E
    Fragment: FAB LIGHT CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FAB OF THE V3-30/ VH1.9III-ENCODED 2A2 IGM RHEUMATOID FACTOR PRODUCED BY TRYPSIN CLEAVAGE OF THE IGM SECRETED BY A HYBRIDOMA CREATED FROM SYNOVIAL B CELLS OF A RHEUMATOID ARTHRITIS PATIENT
 
Molecule 2 - IGM RF 2A2
    Chains: B, D, F
    Fragment: FAB HEAVY CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FAB OF THE V3-30/ VH1.9III-ENCODED 2A2 IGM RHEUMATOID FACTOR PRODUCED BY TRYPSIN CLEAVAGE OF THE IGM SECRETED BY A HYBRIDOMA CREATED FROM SYNOVIAL B CELLS OF A RHEUMATOID ARTHRITIS PATIENT
 
Molecule 3 - IMMUNOGLOBULIN G BINDING PROTEIN A
    Chains: G, H
    Engineered: YES
    Expression System: STAPHYLOCOCCUS AUREUS
    Expression System Taxid: 1280
    Fragment: RECOMBINANT DOMAIN D
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD  G 
Biological Unit 3 (1x):     EF H
Biological Unit 4 (1x):     EF  
Biological Unit 5 (1x):   CD    

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DEE)

(-) Sites  (0, 0)

(no "Site" information available for 1DEE)

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:635
4B:522 -B:596
5B:648 -B:708
6C:1023 -C:1088
7C:1134 -C:1194
8C:1214 -D:1635
9D:1522 -D:1596
10D:1648 -D:1708
11E:2023 -E:2088
12E:2134 -E:2194
13E:2214 -F:2635
14F:2522 -F:2596
15F:2648 -F:2708

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Ala A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Leu B:654 -Pro B:655
5Ser C:1007 -Pro C:1008
6Ala C:1094 -Pro C:1095
7Tyr C:1140 -Pro C:1141
8Leu D:1654 -Pro D:1655
9Ser E:2007 -Pro E:2008
10Ala E:2094 -Pro E:2095
11Tyr E:2140 -Pro E:2141
12Leu F:2654 -Pro F:2655

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DEE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DEE)

(-) Exons   (0, 0)

(no "Exon" information available for 1DEE)

(-) 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:214
                                                                                                                                                                                                                                                       
               SCOP domains d1deea1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1deea2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1deeA01 A:1-107 Immunoglobulins                                                                            1deeA02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee...ee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dee A    1 DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains d1deeb1 B:501-621 Immunoglobulin heavy chain variable domain, VH                                                         d1deeb2 B:622-723 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                              SCOP domains
               CATH domains 1deeB01 B:501-621 Immunoglobulins                                                                                        1deeB02 B:622-723 Immunoglobulins                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeeee.........eeeeeeeeeee.....eeeee.........eee...eee..eeeeeeeeeee..........eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dee B  501 QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVSSGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVAQGTNEHVVCKVQHPNGNKEKDVPL  723
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720   


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1deec1 C:1001-1107 Immunoglobulin light chain kappa variable domain, VL-kappa                             d1deec2 C:1108-1214 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1deeC01 C:1001-1108 Immunoglobulins                                                                         1deeC02 C:1109-1211 Immunoglobulins                                                                    --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dee C 1001 DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 1214
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210    


Chain D from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains d1deed1 D:1501-1621 Immunoglobulin heavy chain variable domain, VH                                                       d1deed2 D:1622-1723 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                            SCOP domains
               CATH domains 1deeD01 D:1501-1621 Immunoglobulins                                                                                      1deeD02 D:1622-1723 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...........ee...eeeee........eeeeee.........eeeeeeeeeee.....eeeee.........eee...eee..eeeeeeeeeee..........eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dee D 1501 QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVSSGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVAQGTNEHVVCKVQHPNGNKEKDVPL 1723
                                  1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710      1720   


Chain E from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1deee1 E:2001-2107 Immunoglobulin light chain kappa variable domain, VL-kappa                             d1deee2 E:2108-2214 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1deeE01 E:2001-2107 Immunoglobulins                                                                        1deeE02 E:2108-2211 Immunoglobulins                                                                     --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dee E 2001 DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2214
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210    


Chain F from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains d1deef1 F:2501-2621 Immunoglobulin heavy chain variable domain, VH                                                       d1deef2 F:2622-2723 Immunoglobulin heavy chain mu constant domain 1, CH1-mu                            SCOP domains
               CATH domains 1deeF01 F:2501-2621 Immunoglobulins                                                                                      1deeF02 F:2622-2723 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeeee.........eeeeeeeeeee.....eeeee.........eee...eee..eeeeeeeeeee..........eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dee F 2501 QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVSSGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVAQGTNEHVVCKVQHPNGNKEKDVPL 2723
                                  2510      2520      2530      2540      2550      2560      2570      2580      2590      2600      2610      2620      2630      2640      2650      2660      2670      2680      2690      2700      2710      2720   


Chain G from PDB  Type:PROTEIN  Length:51
 aligned with SPA_STAA8 | P02976 from UniProtKB/Swiss-Prot  Length:516

    Alignment length:51
                                   112       122       132       142       152 
           SPA_STAA8    103 DQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPK  153
               SCOP domains d1deeg_ G: Immunoglobulin-binding protein A modules SCOP domains
               CATH domains 1deeG00 G:1806-1856 Immunoglobulin FC, subunit C    CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                1dee G 1806 DQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPK 1856
                                  1815      1825      1835      1845      1855 


Chain H from PDB  Type:PROTEIN  Length:54
 aligned with SPA_STAA8 | P02976 from UniProtKB/Swiss-Prot  Length:516

    Alignment length:54
                                   109       119       129       139       149    
           SPA_STAA8    100 FNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPK  153
               SCOP domains d1deeh_ H: Immunoglobulin-binding protein A modules    SCOP domains
               CATH domains 1deeH00 H:2803-2856 Immunoglobulin FC, subunit C       CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                1dee H 2803 FNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPK 2856
                                  2812      2822      2832      2842      2852
   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  (5, 14)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 14)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
2a1deeC02C:1109-1211
2b1deeB01B:501-621
2c1deeD01D:1501-1621
2d1deeF01F:2501-2621
2e1deeB02B:622-723
2f1deeD02D:1622-1723
2g1deeF02F:2622-2723
2h1deeA02A:108-211
2i1deeE02E:2108-2211
2j1deeA01A:1-107
2k1deeE01E:2001-2107
2l1deeC01C:1001-1108

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DEE)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain G,H   (SPA_STAA8 | P02976)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
    GO:0019865    immunoglobulin binding    Interacting selectively and non-covalently with an immunoglobulin.
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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1dee
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  SPA_STAA8 | P02976
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPA_STAA8 | P02976: 1fc2 1h0t 4y4y 4y5z

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DEE)