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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 :  23 Sep 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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 , PHE A:386 , PRO A:387BINDING SITE FOR RESIDUE IMD A1476

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:94 -A:247
2A:162 -A:192
3A:208 -A:220
4A:265 -A:363
5A:282 -A:354
6A:388 -A:444
7A:432 -A:449
8A: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 1W8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W8K)

(-) Exons   (0, 0)

(no "Exon" information available for 1W8K)

(-) 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:362
 aligned with O61130_PLAVI | O61130 from UniProtKB/TrEMBL  Length:562

    Alignment length:433
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472   
         O61130_PLAVI    43 PTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSSYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKNESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKSAFLPVGAFNSDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISNSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYYE 475
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------AMA-1-1w8kA01 A:55-475                                                                                                                                                                                                                                                                                                                                                                                                                Pfam domains
         Sec.struct. author .eeee.......hhhhhh..hhhhhh.........eeee....eeee......ee.eeeee.............-------..............eehhhhhhhh....hhhhhhhhhhhhhhhhh..------......eeee....eeee.........---...------.....eeeee.hhhh.eeee......hhhhhh...eeeeeeeeeee..eee.....eeee..hhhhhhhhhhhhh......--------------------------------------.........eeeee....eeeee.....eeeeeeeeeeee.......ee.....hhhhhhhhhhhh..-----------.eeee....ee.hhhhhh.....ee........ee.......eeeehhheeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8k A  43 PTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVAT-------GGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFV------SNYRHPAVYDEKEKTCHMLYLSAQENM---YCS------DAVFCFKPDKDESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPT--------------------------------------FKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQ-----------ERIVLPRIFISNDKESIKCPCEPERISQSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYYE 475
                                    52        62        72        82        92       102       112   |     - |     132       142       152       162       | -    |  182       192       202|   | |  -   |   222       232       242       252       262       272       282       292   |     -         -         -         -  |    342       352       362       372       382       392       402         - |     422       432       442       452       462       472   
                                                                                                   116     124                                           170    177                       203 207 |    216                                                                             296                                    335                                                                402         414                                                             
                                                                                                                                                                                                209                                                                                                                                                                                                                                                                          


Chain A from PDB  Type:PROTEIN  Length:362
 aligned with Q9TY14_PLAVI | Q9TY14 from UniProtKB/TrEMBL  Length:445

    Alignment length:433
                                    10        20        30        40        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   
         Q9TY14_PLAVI     1 PTVERSTRMGNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSSYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKNESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKSAFLPVGAFNSDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISNSTCNFYVCNCVEKRAEIKENNQVVIKEEFRNYYE 433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------AMA-1-1w8kA01 A:55-475                                                                                                                                                                                                                                                                                                                                                                                                                Pfam domains
         Sec.struct. author .eeee.......hhhhhh..hhhhhh.........eeee....eeee......ee.eeeee.............-------..............eehhhhhhhh....hhhhhhhhhhhhhhhhh..------......eeee....eeee.........---...------.....eeeee.hhhh.eeee......hhhhhh...eeeeeeeeeee..eee.....eeee..hhhhhhhhhhhhh......--------------------------------------.........eeeee....eeeee.....eeeeeeeeeeee.......ee.....hhhhhhhhhhhh..-----------.eeee....ee.hhhhhh.....ee........ee.......eeeehhheeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8k A  43 PTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVAT-------GGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFV------SNYRHPAVYDEKEKTCHMLYLSAQENM---YCS------DAVFCFKPDKDESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPT--------------------------------------FKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQ-----------ERIVLPRIFISNDKESIKCPCEPERISQSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYYE 475
                                    52        62        72        82        92       102       112   |     - |     132       142       152       162       | -    |  182       192       202|   | |  -   |   222       232       242       252       262       272       282       292   |     -         -         -         -  |    342       352       362       372       382       392       402         - |     422       432       442       452       462       472   
                                                                                                   116     124                                           170    177                       203 207 |    216                                                                             296                                    335                                                                402         414                                                             
                                                                                                                                                                                                209
   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 1W8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W8K)

(-) 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   (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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9TY14_PLAVI | Q9TY14: 1w81
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        Q9TY14_PLAVI | Q9TY14: 2j4w

(-) Related Entries Specified in the PDB File

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