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(-) Description

Title :  CO-STRUCTURE OF AN AMA1 MUTANT (Y230A) WITH A SURFACE EXPOSED REGION OF RON2 FROM TOXOPLASMA GONDII
 
Authors :  M. L. Tonkin, M. Roques, M. H. Lamarque, M. Pugniere, D. Douguet, J. Craw M. Lebrun, M. J. Boulanger
Date :  10 Feb 11  (Deposition) - 03 Aug 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Membrane Protein, Moving Junction, Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Tonkin, M. Roques, M. H. Lamarque, M. Pugniere, D. Douguet, J. Crawford, M. Lebrun, M. J. Boulanger
Host Cell Invasion By Apicomplexan Parasites: Insights From The Co-Structure Of Ama1 With A Ron2 Peptide
Science V. 333 463 2011
PubMed-ID: 21778402  |  Reference-DOI: 10.1126/SCIENCE.1204988

(-) Compounds

Molecule 1 - APICAL MEMBRANE ANTIGEN, PUTATIVE
    Chains: A, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH-FIVE
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: DOMAINS I/II/III, RESIDUES 64-484
    Mutation: YES
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811
    Synonym: AMA1, APICAL MEMBRANE ANTIGEN 1
 
Molecule 2 - RHOPTRY NECK PROTEIN 2
    Chains: B, E
    Fragment: RESIDUES 235-271
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811
    Synonym: RON2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1BO32Ligand/IonBORIC ACID
2GOL3Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1BO32Ligand/IonBORIC ACID
2GOL2Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BO3-1Ligand/IonBORIC ACID
2GOL1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:83 , ASN A:86 , HIS A:89 , VAL A:390 , HOH A:2103BINDING SITE FOR RESIDUE NAG A1480
2AC2SOFTWAREPHE A:85 , PRO A:287 , ASN A:288 , GLN A:289BINDING SITE FOR RESIDUE BO3 A1481
3AC3SOFTWAREARG A:292 , GLY A:293 , TYR A:294 , SER A:396 , ASP A:397 , SER A:398 , GLN A:465BINDING SITE FOR RESIDUE BO3 A1482
4AC4SOFTWARELYS A:103 , LYS A:212 , ARG A:214BINDING SITE FOR RESIDUE GOL A1483
5AC5SOFTWAREGLU A:316 , LYS A:327BINDING SITE FOR RESIDUE GOL A1484
6AC6SOFTWAREGLU D:83 , ASN D:86 , HIS D:89 , VAL D:390BINDING SITE FOR RESIDUE NAG D1474
7AC7SOFTWAREASN D:137 , ASP D:220 , ASN D:265 , HIS D:267BINDING SITE FOR RESIDUE GOL D1475

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:117 -A:286
2A:194 -A:226
3A:242 -A:255
4A:304 -A:393
5A:324 -A:384
6A:435 -A:459
7A:447 -A:471
8A:452 -A:479
9B:1313 -B:1323
10D:117 -D:286
11D:194 -D:226
12D:242 -D:255
13D:304 -D:393
14D:324 -D:384
15D:435 -D:459
16D:447 -D:471
17E:1313 -E:1323

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Pro A:132 -Pro A:133
2Asn A:153 -Pro A:154
3Ser A:172 -Pro A:173
4Glu A:247 -Pro A:248
5Pro D:132 -Pro D:133
6Asn D:153 -Pro D:154
7Ser D:172 -Pro D:173
8Glu D:247 -Pro D:248
9Trp D:354 -Pro D:355

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y8S)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y8S)

(-) 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 A from PDB  Type:PROTEIN  Length:386
 aligned with AMA1_TOXGV | B6KAM0 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:411
                                    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       438       448       458       468       478 
          AMA1_TOXGV     69 GNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPHTYPLTSQASWNDWWPLHQSDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC  479
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh................eeeee..eeeee......ee..eeeee................hhhhhhh.......................eehhhhhh.......hhhhhhhhhhhheee.............eeee....eeee.............ee.........eeeeeee........eeeehhhhhh...hhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh........--------------------...........eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh...-----...hhhh.........ee........eeeeeeee..eeeeeeee...hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y8s A   69 GNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILAVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQP--------------------DQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSN-----PTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC  479
                                    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|        -         - |     368       378       388       398       408       418  |    428       438       448       458       468       478 
                                                                                                                                                                                                                                                                                                        339                  360                                                          421   427                                                    


Chain B from PDB  Type:PROTEIN  Length:36
 aligned with RON2_TOXGM | B6KV60 from UniProtKB/Swiss-Prot  Length:1479

    Alignment length:36
                                  1306      1316      1326      
          RON2_TOXGM   1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKAT 1332
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.......eeee...eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                2y8s B 1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKAT 1332
                                  1306      1316      1326      


Chain D from PDB  Type:PROTEIN  Length:391
 aligned with AMA1_TOXGV | B6KAM0 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:405
                                    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       438       448       458       468     
          AMA1_TOXGV     69 GNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPHTYPLTSQASWNDWWPLHQSDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTA  473
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......---hhhhhhh................eeeee..eeeee......ee..eeeee................hhhhhhhhh.....................eehhhhhh.......hhhhhhhhhhhheeee............eeee....eeee.............ee.........eeeeeee........eeeehhhhhh...hhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh...............----....................eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh...-------..............ee........eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y8s D   69 GNPFQA---MKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILAVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPHTYPLTS----NDWWPLHQSDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSN-------PETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTA  473
                                 |  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       | -  |    358       368       378       388       398       408       418  |      -|      438       448       458       468     
                                74  78                                                                                                                                                                                                                                                                         346  351                                                                   421     429                                            


Chain E from PDB  Type:PROTEIN  Length:35
 aligned with RON2_TOXGM | B6KV60 from UniProtKB/Swiss-Prot  Length:1479

    Alignment length:35
                                  1306      1316      1326     
          RON2_TOXGM   1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKA 1331
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.......eeee...eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                2y8s E 1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKA 1331
                                  1306      1316      1326
   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 2Y8S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y8S)

(-) Gene Ontology  (8, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (AMA1_TOXGV | B6KAM0)
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B,E   (RON2_TOXGM | B6KV60)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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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  2y8s
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  AMA1_TOXGV | B6KAM0
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  RON2_TOXGM | B6KV60
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMA1_TOXGV | B6KAM0: 2x2z 2y8r 2y8t
        RON2_TOXGM | B6KV60: 2y8t

(-) Related Entries Specified in the PDB File

2y8r CRYSTAL STRUCTURE OF APO AMA1 MUTANT (TYR230ALA) FROM TOXOPLASMA GONDII
2y8t CO-STRUCTURE OF AMA1 WITH A SURFACE EXPOSED REGION OF RON2 FROM TOXOPLASMA GONDII