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(-) Description

Title :  PFAMA1 IN COMPLEX WITH INVASION-INHIBITORY PEPTIDE R1
 
Authors :  B. Vulliez-Le Normand, F. A. Saul, G. A. Bentley
Date :  07 Jul 11  (Deposition) - 11 Jul 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Ama1, Plasmodium Falciparum, Inhibitory Peptide, Malaria, Cell Invasion, Cell Invasion-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Vulliez-Le Normand, M. L. Tonkin, M. H. Lamarque, S. Langer, S. Hoos, M. Roques, F. A. Saul, B. W. Faber, G. A. Bentley, M. J. Boulanger, M. Lebrun
Structural And Functional Insights Into The Malaria Parasit Moving Junction Complex.
Plos Pathog. V. 8 02755 2012
PubMed-ID: 22737069  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002755

(-) Compounds

Molecule 1 - APICAL MEMBRANE ANTIGEN 1, AMA1
    Chains: A, B
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Fragment: AMA1
    Gene: AMA1, PF11_0344
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7
 
Molecule 2 - R1 PEPTIDE
    Chains: C, D, E, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3SRJ)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:134 , VAL A:137 , THR A:140 , GLN A:141 , TYR A:142 , ALA A:170 , TYR A:175 , PHE A:183 , PHE A:201 , GLY A:222 , ASN A:223 , MET A:224 , ILE A:225 , ASP A:227 , ASN A:228 , SER A:232 , TYR A:234 , LYS A:235 , TYR A:236 , TYR A:251 , ALA A:254 , MET A:273 , GLY B:139 , HOH C:33 , HOH C:181 , HOH C:184 , HOH C:219 , HOH C:248 , HOH C:277 , HOH C:300 , HOH C:365 , HOH C:438 , HOH C:440 , HOH C:666 , LEU D:6 , PRO D:7 , LEU D:8 , PHE D:9 , SER D:10 , VAL F:1BINDING SITE FOR CHAIN C OF R1 PEPTIDE
2AC2SOFTWARETHR A:171 , PRO A:184 , PRO A:185 , THR A:186 , GLU A:187 , MET A:190 , ASN A:228 , LYS A:230 , PHE C:9 , SER C:10 , LYS C:11 , PHE C:12 , GLY C:13 , SER C:14 , HIS C:17 , HOH D:287 , VAL F:1 , PHE F:2BINDING SITE FOR CHAIN D OF R1 PEPTIDE
3AC3SOFTWAREASN A:173 , GLN A:174 , ASP B:134 , GLN B:141 , TYR B:142 , ALA B:170 , TYR B:175 , LEU B:176 , GLY B:222 , ASN B:223 , MET B:224 , ILE B:225 , PRO B:226 , ASP B:227 , ASN B:228 , SER B:232 , TYR B:234 , LYS B:235 , TYR B:236 , TYR B:251 , ALA B:254 , TYR B:262 , MET B:273 , HOH B:626 , HOH E:86 , HOH E:192 , HOH E:364 , LEU F:6 , PRO F:7 , LEU F:8 , PHE F:9BINDING SITE FOR CHAIN E OF R1 PEPTIDE
4AC4SOFTWARETHR A:171 , GLY A:172 , ASN A:173 , PRO B:184 , PRO B:185 , THR B:186 , GLU B:187 , ASN B:228 , LYS B:230 , SER C:10 , GLU D:4 , PHE E:9 , SER E:10 , LYS E:11 , PHE E:12 , GLY E:13 , SER E:14 , HOH F:341BINDING SITE FOR CHAIN F OF R1 PEPTIDE

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:149 -A:302
2A:217 -A:247
3A:263 -A:275
4A:320 -A:418
5A:337 -A:409
6B:149 -B:302
7B:217 -B:247
8B:263 -B:275
9B:320 -B:418
10B:337 -B:409

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Glu A:187 -Pro A:188
2Ser A:191 -Pro A:192
3Glu B:187 -Pro B:188
4Ser B:191 -Pro B:192
5Ala F:3 -Glu F:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SRJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SRJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3SRJ)

(-) 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:298
 aligned with Q7KQK5_PLAF7 | Q7KQK5 from UniProtKB/TrEMBL  Length:622

    Alignment length:340
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
         Q7KQK5_PLAF7   106 MGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVENNFPCSL 445
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee............hhhhh..........ee.....eehhhhhhhh.........hhhhhhhhhhh.eee...........eeee....eeee..............-------.....eeee.hhhhh.eeee......hhhhhh...eeeeeeeeeee..eeee....eeee..hhhhhhhhhhhhh.......-----------------------------------...........eeeee....eeeee.....eeeeeeeeeeee.......ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3srj A 106 MGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSKTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYC-------NSMFCFRPAKDISFQNYVYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQ-----------------------------------DRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINDKSYIATTALSHPIEVENNFPSVP 445
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       | -     | 275       285       295       305       315       325       335       345      |  -         -         -         -  |    395       405       415       425       435       445
                                                                                                                                                                                       263     271                                                                              352                                 388                                                         


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q7KQK5_PLAF7 | Q7KQK5 from UniProtKB/TrEMBL  Length:622

    Alignment length:340
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
         Q7KQK5_PLAF7   106 MGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVENNFPCSL 445
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh.........eeeee..eeeee......ee.eeeee............hhhhh..........ee.....eehhhhhhhh..hhhhhh.hhhhhhhhhhhheee...........eeee....eeee..............--------....eeeee.hhhh.eeee......hhhhhh...eeeeeeeeeee..eeee....eeee..hhhhhhhhhhhhh.......-----------------------------------...........eeeee....eeeee.....eeeeeeeeeeee.......ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3srj B 106 MGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSKTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYC--------SMFCFRPAKDISFQNYVYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQ-----------------------------------DRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINDKSYIATTALSHPIEVENNFPSVP 445
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       | -      |275       285       295       305       315       325       335       345      |  -         -         -         -  |    395       405       415       425       435       445
                                                                                                                                                                                       263      272                                                                             352                                 388                                                         


Chain C from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ...........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 3srj C   1 VFAEFLPLFSKFGSRMHI  18
                                    10        


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..eeee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3srj D   4 EFLPLFS  10


Chain E from PDB  Type:PROTEIN  Length:17
                                                 
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ...........eee... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 3srj E   1 VFAEFLPLFSKFGSRMH  17
                                    10       


Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....eeee. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 3srj F   1 VFAEFLPLFS  10
                                    10
   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 3SRJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SRJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SRJ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7KQK5_PLAF7 | Q7KQK5: 1z40 2q8a 2q8b 2z8v 2z8w 3zwz 4r19 4r1b 4r1c

(-) Related Entries Specified in the PDB File

1z40 PLASMODIUM FALCIPARUM AMA1
3sri