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(-) Description

Title :  STRUCTURE OF THE IMMUNODOMINANT EPITOPE DISPLAYED BY THE SURFACE ANTIGEN 1 (SAG1) OF TOXOPLASMA GONDII COMPLEXED TO A MONOCLONAL ANTIBODY
 
Authors :  M. Graille, E. A. Stura, M. Bossus, B. H. Muller, O. Letourneur, N Batta Poirot, G. Sibai, D. Rolland, M. H. Le Du, F. Ducancel
Date :  25 Jan 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Toxoplasma Gondii, Recombinant Sag1, Conformational Epitope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Graille, E. A. Stura, M. Bossus, B. H. Muller, O. Letourneur, N. Battail-Poirot, G. Sibai, M. Gauthier, D. Rolland, M. H. Le Du, F. Ducancel
Crystal Structure Of The Complex Between The Monomeric Form Of Toxoplasma Gondii Surface Antigen 1 (Sag1) And A Monoclonal Antibody That Mimics The Human Immune Response
J. Mol. Biol. V. 354 447 2005
PubMed-ID: 16242717  |  Reference-DOI: 10.1016/J.JMB.2005.09.028

(-) Compounds

Molecule 1 - 4F11E12 FAB VARIABLE LIGHT CHAIN REGION
    ChainsA, C
    FragmentFAB FRAGMENT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - 4F11E12 FAB VARIABLE HEAVY CHAIN REGION
    ChainsB, D
    FragmentFAB FRAGMENT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - PROTEIN L
    ChainsE
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKK223-3
    Expression System StrainJM103
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDOMAIN C*
    Organism ScientificFINEGOLDIA MAGNA
    Organism Taxid334413
    StrainATCC 29328
 
Molecule 4 - MAJOR SURFACE ANTIGEN P30
    ChainsF, G
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPTG8639
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentRESIDUES IN DATABASE 50-303
    Organism ScientificTOXOPLASMA GONDII
    Organism Taxid5811
    SynonymSAG1 PROTEIN

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:665BINDING SITE FOR RESIDUE CD B 4001
2AC2SOFTWARESER D:1665BINDING SITE FOR RESIDUE CD D 4002

(-) SS Bonds  (22, 22)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:522 -B:596
4B:645 -B:700
5C:1023 -C:1088
6C:1134 -C:1194
7D:1522 -D:1596
8D:1645 -D:1700
9F:2012 -F:2122
10F:2012 -F:2113
11F:2034 -F:2113
12F:2054 -F:2062
13F:2142 -F:2247
14F:2167 -F:2237
15F:2182 -F:2190
16G:3012 -G:3122
17G:3012 -G:3113
18G:3034 -G:3113
19G:3054 -G:3062
20G:3142 -G:3247
21G:3167 -G:3237
22G:3182 -G:3190

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Leu A:94 -Pro A:95
2Tyr A:140 -Pro A:141
3Phe B:651 -Pro B:652
4Trp B:693 -Pro B:694
5Leu C:1094 -Pro C:1095
6Tyr C:1140 -Pro C:1141
7Phe D:1651 -Pro D:1652
8Trp D:1693 -Pro D:1694
9Gly F:2151 -Pro F:2152
10Gly F:2159 -Pro F:2160
11Val F:2174 -Pro F:2175
12Ser F:2241 -Pro F:2242
13Gly G:3151 -Pro G:3152
14Gly G:3159 -Pro G:3160
15Val G:3174 -Pro G:3175
16Ser G:3241 -Pro G:3242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YNT)

(-) 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:213
                                                                                                                                                                                                                                                      
               SCOP domains d1ynta1 A:1-107 automated matches                                                                          d1ynta2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains 1yntA01 A:1-107 Immunoglobulins                                                                            1yntA02 A:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee........eeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...ee..........eeee...hhhhhh..ee..eeeeeee.....ee..ee..ee....eeeee.........eeeeeee.eehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynt A    1 DIQVTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    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:218
                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------d1yntb1 B:619-718 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1yntB01 B:501-618 Immunoglobulins                                                                                     1yntB02 B:619-718 Immunoglobulins                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eee..eee.......eeeeeee......eeeeeee.....ee.hhhhh....eeeehhhheeeeee........eeeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.........eeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynt B  501 QVQLQQSGAELVRPGVSVKISCKGSGYTFTDYGMHWVKQSHAKSLEWIGIISTYSGDASYNQKFKGKATMTVDKSSSTAYMELARLTSEDSAIYYCARSSTWYYFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  718
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710        

Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1yntc1 C:1001-1107 automated matches                                                                      d1yntc2 C:1108-1213 automated matches                                                                      SCOP domains
               CATH domains 1yntC01 C:1001-1107 Immunoglobulins                                                                        1yntC02 C:1108-1211 Immunoglobulins                                                                     -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...ee..........eeee...hhhhhh..ee..eeeeeee.....ee..ee..ee....eeeee.........eeeeeee.eehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynt C 1001 DIQVTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 1213
                                  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:218
                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------d1yntd1 D:1619-1718 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 1yntD01 D:1501-1618 Immunoglobulins                                                                                   1yntD02 D:1619-1718 Immunoglobulins                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eee..eee.......eeeeeee......eeeeee......ee.hhhhh....eeeehhhheeeeee........eeeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....eeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynt D 1501 QVQLQQSGAELVRPGVSVKISCKGSGYTFTDYGMHWVKQSHAKSLEWIGIISTYSGDASYNQKFKGKATMTVDKSSSTAYMELARLTSEDSAIYYCARSSTWYYFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 1718
                                  1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710        

Chain E from PDB  Type:PROTEIN  Length:61
 aligned with Q51918_FINMA | Q51918 from UniProtKB/TrEMBL  Length:992

    Alignment length:61
                                   485       495       505       515       525       535 
        Q51918_FINMA    476 EVTIKVNLIFADGKTQTAEFKGTFEEATAEAYRYADLLAKVNGEYTADLEDGGYTINIKFA  536
               SCOP domains d1ynte_ E:                                                    SCOP domains
               CATH domains 1yntE00 E:820-880  [code=3.10.20.10, no name defined]         CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                1ynt E  820 EVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYADLLAKVNGEYTADLEDGGNHMNIKFA  880
                                   829       839       849       859       869       879 

Chain F from PDB  Type:PROTEIN  Length:252
 aligned with P30_TOXGO | P13664 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:252
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
           P30_TOXGO     51 PLVANQVVTCPDKKSTAAVILTPTENHFTLKCPKTALTEPPTLAYSPNRQICPAGTTSSCTSKAVTLSSLIPEAEDSWWTGDSASLDTAGIKLTVPIEKFPVTTQTFVVGCIKGDDAQSCMVTVTVQARASSVVNNVARCSYGADSTLGPVKLSAEGPTTMTLVCGKDGVKVPQDNNQYCSGTTLTGCNEKSFKDILPKLTENPWQGNASSDKGATLTIKKEAFPAESKSVIIGCTGGSPEKHHCTVKLEFA  302
               SCOP domains d1yntf1 F:2003-2131 automated matches                                                                                            d1yntf2 F:2132-2254 automated matches                                                                                       SCOP domains
               CATH domains 1yntF01 F:2003-2131  [code=2.60.40.1320, no name defined]                                                                        1yntF02 F:2132-2254  [code=2.60.40.1320, no name defined]                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee..eee.......eeeee.......eee.....ee.hhhhhh....................hhhhh....hhh.eee.........eee..hhhhh....eeee..ee.........eeeee.....ee...eee......eeeeeee.......eeeee....eeee...........hhhhh...........................eee..........eeeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1ynt F 2003 PLVANQVVTCPDKKSTAAVILTPTENHFTLKCPKTALTEPPTLAYSPNRQICPAGTTSSCTSKAVTLSSLIPEAEDSWWTGDSASLDTAGIKLTVPIEKFPVTTQTFVVGCIKGDDAQSCMVTVTVQARASSVVNNVARCSYGADSTLGPVKLSAEGPTTMTLVCGKDGVKVPQDNNQYCSGTTLTGCNEKSFKDILPKLTENPWQGNASSDKGATLTIKKEAFPAESKSVIIGCTGGSPEKHHCTVKLEFA 2254
                                  2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122      2132      2142      2152      2162      2172      2182      2192      2202      2212      2222      2232      2242      2252  

Chain G from PDB  Type:PROTEIN  Length:252
 aligned with P30_TOXGO | P13664 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:252
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
           P30_TOXGO     51 PLVANQVVTCPDKKSTAAVILTPTENHFTLKCPKTALTEPPTLAYSPNRQICPAGTTSSCTSKAVTLSSLIPEAEDSWWTGDSASLDTAGIKLTVPIEKFPVTTQTFVVGCIKGDDAQSCMVTVTVQARASSVVNNVARCSYGADSTLGPVKLSAEGPTTMTLVCGKDGVKVPQDNNQYCSGTTLTGCNEKSFKDILPKLTENPWQGNASSDKGATLTIKKEAFPAESKSVIIGCTGGSPEKHHCTVKLEFA  302
               SCOP domains d1yntg1 G:3003-3131 automated matches                                                                                            d1yntg2 G:3132-3254 automated matches                                                                                       SCOP domains
               CATH domains 1yntG01 G:3003-3131  [code=2.60.40.1320, no name defined]                                                                        1yntG02 G:3132-3254  [code=2.60.40.1320, no name defined]                                                                   CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------SAG-1yntG01 G:3136-3253                                                                                               - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------SAG-1yntG02 G:3136-3253                                                                                               - Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------SAG-1yntG03 G:3136-3253                                                                                               - Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------SAG-1yntG04 G:3136-3253                                                                                               - Pfam domains (4)
         Sec.struct. author ..ee..eee.......eeeee.......eee.....ee.hhhhhh....................hhhhh....hhh.eee.........eee..hhhhh....eeee..ee.........eeeee.....ee...eee......eeeeeee.......eeeee....eeee...........hhhhh...........................eee..........eeeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1ynt G 3003 PLVANQVVTCPDKKSTAAVILTPTENHFTLKCPKTALTEPPTLAYSPNRQICPAGTTSSCTSKAVTLSSLIPEAEDSWWTGDSASLDTAGIKLTVPIEKFPVTTQTFVVGCIKGDDAQSCMVTVTVQARASSVVNNVARCSYGADSTLGPVKLSAEGPTTMTLVCGKDGVKVPQDNNQYCSGTTLTGCNEKSFKDILPKLTENPWQGNASSDKGATLTIKKEAFPAESKSVIIGCTGGSPEKHHCTVKLEFA 3254
                                  3012      3022      3032      3042      3052      3062      3072      3082      3092      3102      3112      3122      3132      3142      3152      3162      3172      3182      3192      3202      3212      3222      3232      3242      3252  

   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, 11)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 13)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)
2a1yntF02F:2132-2254
2b1yntG02G:3132-3254
2c1yntF01F:2003-2131
2d1yntG01G:3003-3131
3a1yntA02A:108-211
3b1yntB02B:619-718
3c1yntD02D:1619-1718
3d1yntB01B:501-618
3e1yntD01D:1501-1618
3f1yntC02C:1108-1211
3g1yntA01A:1-107
3h1yntC01C:1001-1107

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Family: SAG (5)
1aSAG-1yntG01G:3136-3253
1bSAG-1yntG02G:3136-3253
1cSAG-1yntG03G:3136-3253
1dSAG-1yntG04G:3136-3253

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (Q51918_FINMA | Q51918)
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.

Chain F,G   (P30_TOXGO | P13664)
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0020003    symbiont-containing vacuole    Membrane-bounded vacuole within a host cell in which a symbiont organism resides. The vacuole membrane is derived from both the host and symbiont.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P30_TOXGO | P136641kzq
UniProtKB/TrEMBL
        Q51918_FINMA | Q519181hez 1ymh 2fs1 4hjg 4hkz 4ioi

(-) Related Entries Specified in the PDB File

1kzq CRYSTAL STRUCTURE OF A PARASITE PROTEIN