Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) 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) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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: 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
    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 2Q8B)

(-) Sites  (0, 0)

(no "Site" information available for 2Q8B)

(-) SS Bonds  (9, 9)

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

(-) 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 2Q8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q8B)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q8B)

(-) 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:292
 aligned with AMA1_PLAFF | P22621 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:334
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
           AMA1_PLAFF   105 YMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFSAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----AMA-1-2q8bA01 A:110-438                                                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee................hhhhh.............eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh........eeee....eeee..............---------...eeee.hhhhh.eeee......hhhhhh....ee..eeeee....eee....eeee..hhhhhhhhhhhhh.........---------------------------------...........eeeee....eeeee.....eee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8b A 105 YMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYC---------MFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYE---------------------------------DRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        |-       274       284       294       304       314       324       334       344       354         -         -         -   |   394       404       414       424       434    
                                                                                                                                                                                        263       273                                                                              354                               388                                                  


Chain A from PDB  Type:PROTEIN  Length:292
 aligned with Q7KQK5_PLAF7 | Q7KQK5 from UniProtKB/TrEMBL  Length:622

    Alignment length:334
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
         Q7KQK5_PLAF7   105 YMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----AMA-1-2q8bA01 A:110-438                                                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee................hhhhh.............eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh........eeee....eeee..............---------...eeee.hhhhh.eeee......hhhhhh....ee..eeeee....eee....eeee..hhhhhhhhhhhhh.........---------------------------------...........eeeee....eeeee.....eee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8b A 105 YMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYC---------MFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYE---------------------------------DRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        |-       274       284       294       304       314       324       334       344       354         -         -         -   |   394       404       414       424       434    
                                                                                                                                                                                        263       273                                                                              354                               388                                                  


Chain H from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------d2q8bh1 H:113-210 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma         SCOP domains
               CATH domains 2q8bH01 H:1-112 Immunoglobulins                                                                                 2q8bH02 H:113-208 Immunoglobulins                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..ee...eeeee........eeeee.....eeeeeeeeeee.....eeeee..eeeeeeee..eeeeeeeeeee.........eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8b H   1 EVQLQQSGAELLRPGASVKLSCIVSGFKIKDTSMHWVKQRPEQGLEWIGRIDPANDNSEYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCTLSHFWGQGTTLTVSSAKTTPPSVYPLAPGCSSVTLGCLVKGYFPESVTVTWNSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLE 210
                                    10        20        30        40        50        60        70        80        90       100       110       120      |135       145       161       171       181       191       201         
                                                                                                                                                        127|                  154|                                                 
                                                                                                                                                         133                   161                                                 


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d2q8bl1 L:1-107 automated matches                                                                          d2q8bl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains 2q8bL01 L:1-108 Immunoglobulins                                                                             2q8bL02 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........eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8b L   1 SIVMTQTPKFLPVSAGDRVTIICKASQSVSNDVVWYQQKPGQSPKLLIYYASIRYTGVPDRFTGSGYGTDFTFTISTVQVEDLAVYFCQQGFSSPRTFGGGTKLEINRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2q8b)
 
  Sites
(no "Sites" information available for 2q8b)
 
  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 ]  
    Trp H:187 - Pro H:188   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2q8b
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AMA1_PLAFF | P22621
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  IGG2B_MOUSE | P01867
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q7KQK5_PLAF7 | Q7KQK5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AMA1_PLAFF | P22621
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IGG2B_MOUSE | P01867
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q7KQK5_PLAF7 | Q7KQK5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AMA1_PLAFF | P22621: 1yxe 2q8a
        IGG2B_MOUSE | P01867: 1cbv 1cf8 1cic 1etz 1fj1 1fl3 1hq4 1mam 1nbv 1osp 1ub5 1ub6 1ynk 1ynl 1ztx 2gjz 2gk0 2q8a 2rgs 3cfd 3cfe
UniProtKB/TrEMBL
        Q7KQK5_PLAF7 | Q7KQK5: 1z40 2q8a 2z8v 2z8w 3srj 3zwz 4r19 4r1b 4r1c

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q8B)