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(-) Description

Title :  STRUCTURE OF A PLASMODIUM VIVAX APICAL MEMBRANE ANTIGEN 1-FAB F8.12.19 COMPLEX
 
Authors :  S. Igonet, B. Vulliez-Le Normand, G. Faure, M. M. Riottot, C. H. M. Kocken, A. W. Thomas, G. A. Bentley
Date :  07 Sep 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  D,H,L
Biol. Unit 1:  D,H,L  (3x)
Keywords :  Immunoglobulin Domain, Immunoglobulin C Region, Membrane, Transmembrane, Hypothetical Protein, Antibody Cross- Reactivity, Surface Active Protein, Malaria Vaccine Candidate, Apical Membrane Antigen 1, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Igonet, B. Vulliez-Le Normand, G. Faure, M. M. Riottot, C. H. M. Kocken, A. W. Thomas, G. A. Bentley
Cross-Reactivity Studies Of An Anti-Plasmodium Vivax Apical Membrane Antigen 1 Monoclonal Antibody: Binding And Structural Characterisation.
J. Mol. Biol. V. 366 1523 2007
PubMed-ID: 17229439  |  Reference-DOI: 10.1016/J.JMB.2006.12.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APICAL MEMBRANE ANTIGEN 1
    Chains: D
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PHIL-S1
    Expression System Taxid: 4922
    Mutation: YES
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Strain: SAL I
    Synonym: PLASMODIUM VIVAX APICAL MEMBRANE ANTIGEN 1
 
Molecule 2 - FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
    Chains: H
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA
    Strain: BALB/C
    Synonym: ANTIGEN-BINDING FRAGMENT FAB, HEAVY CHAIN
 
Molecule 3 - FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA
    Strain: BALB/C
    Synonym: ANTIGEN-BINDING FRAGMENT FAB, LIGHT CHAIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : DHL
Biological Unit 1 (3x): DHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1PCA3Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 2J4W)

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1D:432 -D:449
2D:434 -D:451
3H:22 -H:92
4H:142 -H:208
5H:233 -L:214
6L:23 -L:88
7L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe H:148 -Pro H:149
2Glu H:150 -Pro H:151
3Arg H:199 -Pro H:200
4Ser L:7 -Pro L:8
5His L:94 -Pro L:95
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J4W)

(-) Exons   (0, 0)

(no "Exon" information available for 2J4W)

(-) 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 D from PDB  Type:PROTEIN  Length:34
 aligned with Q9TY14_PLAVI | Q9TY14 from UniProtKB/TrEMBL  Length:445

    Alignment length:34
                                   388       398       408    
        Q9TY14_PLAVI    379 IFISNDKESIKCPCEPERISNSTCNFYVCNCVEK  412
               SCOP domains d2j4wd1 D:421-454                  SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh.....eeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                2j4w D  421 IFISNDKESIKCPCEPERISESTCNFYVCNCVEK  454
                                   430       440       450    


Chain H from PDB  Type:PROTEIN  Length:225
 aligned with Q569B4_RAT | Q569B4 from UniProtKB/TrEMBL  Length:468

    Alignment length:231
                                                                                                                                   123                                                                                                                             
                                                                                                                                122  |                                                                                                                             
                                    29        39        49        59        69        79        89        99       109       119  |  | 127       137       147       157       167       177       187       197       207       217       227       237       247 
          Q569B4_RAT     20 EVQILETGGGLVKPGGSLRLSCATSGFNFNDYFMNWVRQAPGKGLEWVVQIRNKNYNYGTYYAESLEGRVTISRDDSKSSVYLQVTSFRPEDTAIYYCTRSRP--YYGYNYFDYWGQGVMVTVSSAETTAPSVYPLAPGTALKSNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRNCGGDC  248
               SCOP domains d2j4wh1 H:1-112 Immunoglobulin heavy chain variable dom ai n, VH                                                            d2j4wh2 H:113-233 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                             SCOP domains
               CATH domains 2j4wH01 H:1-113 Immunoglobulins                                                                                              2j4wH02 H:114-227 Immunoglobulins                                                                  -    -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee....-..-eee.hhhh...eeeee....eeeeee...hhhhheeeeeee.............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee....----.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j4w H    1 EVQLVESGGGLVKPGGSLKLSCAASGFIFSDYYMYWVRQTPEKRLEWVATISDGN-SY-TYYVDSVKGRFTISRDNAKNNLYLQMSSLKSEDTAIYYCARDGPTDSSGYGGFGYWGQGTLVTVSEAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR----DC  233
                                    10        20        30        40        50  | | ||57        67        77     |||84        94      100D||     108       118       128 ||    140       150   ||||165   ||  176   ||  188       199||   ||211       221 || |  232 
                                                                              52A | || |                       82A||               100A|||||                           130|                  154|||    169|      180|          196| || 206|            223| |  232 
                                                                                 54 || |                        82B|                100B||||                            133                   156||     171       183           198 ||  208             226 |      
                                                                                   55| |                         82C                 100C|||                                                   157|                               200|                    228      
                                                                                    56 |                                              100D||                                                    162                                202                             
                                                                                      57                                               100E|                                                                                                                       
                                                                                                                                        100F                                                                                                                       


Chain L from PDB  Type:PROTEIN  Length:213
 aligned with Q5XFY8_MOUSE | Q5XFY8 from UniProtKB/TrEMBL  Length:235

    Alignment length:221
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
        Q5XFY8_MOUSE     15 ASVIMSRGQIVLSQSPAILSGFPGEKVTMTCRASSSVNYMHWYQQKPGSSPKPWIYATSKLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSNPLTFGAGTRLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  235
               SCOP domains d2        j4wl1 L:1-107 automated matches                                                                         d2j4wl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains -2        j4wL01 L:2-108 Immunoglobulins                                                                           2j4wL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------.eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee....ee..eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j4w L    1 xS--------VLSQSPAILSASPGEKVTMTCRARSSVSYMHWYQQKSGSSPKPWIHATSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSHPPTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                            ||       -|       12        22    ||  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
                            ||        3                      27|                                                                                                                                                                                         
                            1-PCA                             29                                                                                                                                                                                         
                             2
   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, 5)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J4W)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain D   (Q9TY14_PLAVI | Q9TY14)
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain H   (Q569B4_RAT | Q569B4)

Chain L   (Q5XFY8_MOUSE | Q5XFY8)

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  Cis Peptide Bonds
    Arg H:199 - Pro H:200   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    His L:94 - Pro L:95   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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  2j4w
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  Q5XFY8_MOUSE | Q5XFY8
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  Q9TY14_PLAVI | Q9TY14
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q569B4_RAT | Q569B4: 2hfe
        Q9TY14_PLAVI | Q9TY14: 1w81 1w8k
UniProtKB/TrEMBL
        Q569B4_RAT | Q569B4: 2h8p 2hg5
        Q5XFY8_MOUSE | Q5XFY8: 2j5l 3oz9

(-) Related Entries Specified in the PDB File

1w81 CRYSTAL STRUCTURE OF APICAL MEMBRANE ANTIGEN 1 FROM PLASMODIUM VIVAX
1w8k CRYSTAL STRUCTURE OF APICAL MEMBRANE ANTIGEN 1 FROM PLASMODIUM VIVAX