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(-) Description

Title :  STRUCTURE OF THE MALARIA ANTIGEN AMA1 IN COMPLEX WITH A GROWTH-INHIBITORY ANTIBODY
 
Authors :  A. Gupta, V. J. Murphy, R. F. Anders, A. H. Batchelor
Date :  10 Jun 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Antigen-Antibody Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Coley, A. Gupta, V. J. Murphy, T. Bai, H. Kim, M. Foley, R. F. Anders A. H. Batchelor
Structure Of The Malaria Antigen Ama1 In Complex With A Growth-Inhibitory Antibody
Plos Pathog. V. 3 E138 2007
PubMed-ID: 17907804  |  Reference-DOI: DOI:10.1371/JOURNAL.PPAT.0030138

(-) Compounds

Molecule 1 - APICAL MEMBRANE ANTIGEN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PPROEXHTB
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: DOMAINS I AND II (RESIDUES 104-438)
    Gene: AMA1
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7
 
Molecule 2 - 1F9 LIGHT CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA CELL LINE
 
Molecule 3 - 1F9 HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA CELL LINE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Q8A)

(-) Sites  (0, 0)

(no "Site" information available for 2Q8A)

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:149 -A:302
2A:217 -A:247
3A:263 -A:275
4A:320 -A:418
5A:337 -A:409
6H:22 -H:96
7H:139 -H:194
8L:23 -L:88
9L:134 -L:194
10L:214 -H:127

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Glu A:187 -Pro A:188
2Ser A:191 -Pro A:192
3Thr L:7 -Pro L:8
4Ser L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Phe H:145 -Pro H:146
7Trp H:187 -Pro H:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q8A)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q8A)

(-) 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:316
 aligned with AMA1_PLAFF | P22621 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:332
                                   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  
           AMA1_PLAFF   107 GNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFSAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---AMA-1-2q8aA01 A:110-438                                                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee................hhhhh.............eehhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhh........eeee....eeee..........................eeee.hhhhh.eeee......hhhhhh....ee..eeeeee..eeee....eeee..hhhhhhhhhhhhh.....---....hhhhhhhh...........-------------.........eeeee....eeeee.....eee....eeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8a A 107 GNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQP---EQHLTDYEKIKEGFKNKNASMIK-------------YKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
                                   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         -   |   396       406       416       426       436  
                                                                                                                                                                                                                                                                             350 354                   376           390                                                


Chain A from PDB  Type:PROTEIN  Length:316
 aligned with Q7KQK5_PLAF7 | Q7KQK5 from UniProtKB/TrEMBL  Length:622

    Alignment length:332
                                   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  
         Q7KQK5_PLAF7   107 GNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---AMA-1-2q8aA01 A:110-438                                                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee................hhhhh.............eehhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhh........eeee....eeee..........................eeee.hhhhh.eeee......hhhhhh....ee..eeeeee..eeee....eeee..hhhhhhhhhhhhh.....---....hhhhhhhh...........-------------.........eeeee....eeeee.....eee....eeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8a A 107 GNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQP---EQHLTDYEKIKEGFKNKNASMIK-------------YKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
                                   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         -   |   396       406       416       426       436  
                                                                                                                                                                                                                                                                             350 354                   376           390                                                


Chain H from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------d2q8ah1 H:113-208 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma         SCOP domains
               CATH domains 2q8aH01 H:1-112 Immunoglobulins                                                                                 2q8aH02 H:113-208 Immunoglobulins                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeee..ee...eeeee........eeeee......eeeeeeeeeee.....eeeee..eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8a H   1 EVQLQQSGAELLKPGASVKLSCIVSGFKIKDTSMHWVKQRPEQGLEWIGRIDPANDNSEYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCTLSHFWGQGTTLTVSSAKTTPPSVYPLAPGCGSSVTLGCLVKGYFPESVTVTWNSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKK 208
                                    10        20        30        40        50        60        70        80        90       100       110       120      |134       144       154|      169       179       189       199         
                                                                                                                                                        127|                   154|                                                
                                                                                                                                                         132                    160                                                


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d2q8al1 L:1-107 automated matches                                                                          d2q8al2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains 2q8aL01 L:1-108 Immunoglobulins                                                                             2q8aL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8a L   1 SIVMTQTPKFLPVSAGDRVTIICKASQSVSNDVVWYQQKPGQSPKLLIYYASIRYTGVPDRFTGSGYGTDFTFTISTVQVEDLAVYFCQQGFSSPRTFGGGTKLEINRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (3, 3)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: AMA-1] (6)

(-) Gene Ontology  (29, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7KQK5_PLAF7 | Q7KQK5)
molecular function
    GO:0046812    host cell surface binding    Interacting selectively and non-covalently with the surface of a host cell.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030260    entry into host cell    The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0020007    apical complex    A group of cytoskeletal structures and associated membrane-bounded organelles found at the anterior end of adult obligate intracellular protozoan parasites in the phylum Apicomplexa. The apical complex is involved in attachment to and penetration of the host cell, and in parasite proliferation.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0020009    microneme    A small, elongated secretory organelle that forms part of the apical complex, located along the main axis of an apicomplexan parasite cell within the extreme apical region and at the periphery under the inner membrane complex. Of the specialized secretory compartments identified in apicomplexans, micronemes discharge their contents first, during initial contact of the parasite's apical pole with the host cell surface. Micronemal proteins function during parasite attachment and penetration into the target cell.

Chain A   (AMA1_PLAFF | P22621)
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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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  Cis Peptide Bonds
    Glu A:187 - Pro A:188   [ RasMol ]  
    Phe H:145 - Pro H:146   [ RasMol ]  
    Ser A:191 - Pro A:192   [ RasMol ]  
    Ser L:94 - Pro L:95   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  2q8a
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  AMA1_PLAFF | P22621
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  IGG2B_MOUSE | P01867
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  Q7KQK5_PLAF7 | Q7KQK5
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMA1_PLAFF | P22621: 1yxe 2q8b
        IGG2B_MOUSE | P01867: 1cbv 1cf8 1cic 1etz 1fj1 1fl3 1hq4 1mam 1nbv 1osp 1ub5 1ub6 1ynk 1ynl 1ztx 2gjz 2gk0 2q8b 2rgs 3cfd 3cfe
UniProtKB/TrEMBL
        Q7KQK5_PLAF7 | Q7KQK5: 1z40 2q8b 2z8v 2z8w 3srj 3zwz 4r19 4r1b 4r1c

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q8A)