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(-) Description

Title :  CRYSTAL STRUCTURE OF APICAL MEMBRANE ANTIGEN 1 FROM PLASMODIUM VIVAX
 
Authors :  J. C. Pizarro, B. Vulliez-Le Normand, M. -L. Chesne-Seck, C. H. M. Kocken, A. W. Thomas, G. A. Bentley
Date :  15 Sep 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Plasmodium Antigen, Malaria Vaccine Candidate, Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Pizarro, B. Vulliez-Le Normand, M. -L. Chesne-Seck, C. Collins, C. Withers-Martinez, F. Hackett, M. Blackman, B. Faber, E. Remarque, C. H. M. Kocken, A. W. Thomas, G. A. Bentley
Crystal Structure Of The Malaria Vaccine Candidate Apical Membrane Antigen 1
Science V. 308 408 2005
PubMed-ID: 15731407  |  Reference-DOI: 10.1126/SCIENCE.1107449

(-) Compounds

Molecule 1 - APICAL MEMBRANE ANTIGEN 1
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Fragment: ECTOPLASMIC REGION, RESIDUES 1-445
    Mutation: YES
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Strain: SAL I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:252 , GLY A:253 , LEU A:364 , ASP A:383 , GLU A:385 , PRO A:387 , HOH A:2288BINDING SITE FOR RESIDUE IMD A1475

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:94 -A:247
2A:162 -A:192
3A:265 -A:363
4A:282 -A:354
5A:388 -A:444
6A:432 -A:449
7A:434 -A:451

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:136 -Pro A:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W81)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W81)

(-) Exons   (0, 0)

(no "Exon" information available for 1W81)

(-) 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:364
 aligned with O61130_PLAVI | O61130 from UniProtKB/TrEMBL  Length:562

    Alignment length:434
                                    50        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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470    
         O61130_PLAVI    41 KGPTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSSYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKNESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKSAFLPVGAFNSDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISNSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYY 474
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------AMA-1-1w81A01 A:55-474                                                                                                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ...eeee.......hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee..................................eehhhhhhhh..hhhhhhhhhhhhhhhhhhh..----........eeee....eeee..........--------------..eeee.hhhhh.eeee......hhhhhh...eeeeeeeeeee..eee.....eeee..hhhhhhhhhhhhh....----------------------------------------.........eeeee....eeeee.....eeeeeeeeeeee.......ee.....hhhhhhhhhhhh------------..eeee....ee.hhhhhh.....ee........ee.......eeeehhheeee.hhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w81 A  41 SIPTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFV----QNSNYRHPAVYDEKEKTCHMLYLSAQENMG--------------FCFKPDKDESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQ----------------------------------------FKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIK------------GERIVLPRIFISNDKESIKCPCEPERISQSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYY 474
                                    50        60        70        80        90       100       110       120       130       140       150       160       170    |  180       190       200   |     -       220       230       240       250       260       270       280       290   |     -         -         -         -    |  340       350       360       370       380       390       400         -  |    420       430       440       450       460       470    
                                                                                                                                                           170  175                          204            219                                                                        294                                      335                                                              400          413                                                             


Chain A from PDB  Type:PROTEIN  Length:364
 aligned with Q9TY14_PLAVI | Q9TY14 from UniProtKB/TrEMBL  Length:445

    Alignment length:434
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428    
         Q9TY14_PLAVI     - --PTVERSTRMGNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSSYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKNESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKSAFLPVGAFNSDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISNSTCNFYVCNCVEKRAEIKENNQVVIKEEFRNYY 432
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------AMA-1-1w81A01 A:55-474                                                                                                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ...eeee.......hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee..................................eehhhhhhhh..hhhhhhhhhhhhhhhhhhh..----........eeee....eeee..........--------------..eeee.hhhhh.eeee......hhhhhh...eeeeeeeeeee..eee.....eeee..hhhhhhhhhhhhh....----------------------------------------.........eeeee....eeeee.....eeeeeeeeeeee.......ee.....hhhhhhhhhhhh------------..eeee....ee.hhhhhh.....ee........ee.......eeeehhheeee.hhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w81 A  41 SIPTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFV----QNSNYRHPAVYDEKEKTCHMLYLSAQENMG--------------FCFKPDKDESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQ----------------------------------------FKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIK------------GERIVLPRIFISNDKESIKCPCEPERISQSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYY 474
                                    50        60        70        80        90       100       110       120       130       140       150       160       170    |  180       190       200   |     -       220       230       240       250       260       270       280       290   |     -         -         -         -    |  340       350       360       370       380       390       400         -  |    420       430       440       450       460       470    
                                                                                                                                                           170  175                          204            219                                                                        294                                      335                                                              400          413
   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  (0, 0)

(no "SCOP Domain" information available for 1W81)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W81)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (3, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 A   (O61130_PLAVI | O61130)
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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  1w81
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9TY14_PLAVI | Q9TY14: 1w8k
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        O61130_PLAVI | O61130: 1w8k
        Q9TY14_PLAVI | Q9TY14: 2j4w

(-) Related Entries Specified in the PDB File

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