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(-) Description

Title :  CRYSTAL STRUCTURE OF PFEBA-175 RII IN COMPLEX WITH A FAB FRAGMENT FROM INHIBITORY ANTIBODY R217
 
Authors :  E. Chen, M. M. Paing, N. Salinas, B. K. Sim, N. H. Tolia
Date :  19 May 14  (Deposition) - 04 Jun 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.50
Chains :  Asym. Unit :  A,B,H,I,L,M
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  B,I,M  (1x)
Keywords :  Duffy Binding Like (Dbl) Domain, Immunoglobulin Domain, Invasion, Adhesion, Immunity, Pfeba-175, Antibody, Cell Surface, Extrecellular, Cell Adhesion, Receptor, Ligand, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Chen, M. M. Paing, N. Salinas, B. K. Sim, N. H. Tolia
Structural And Functional Basis For Inhibition Of Erythrocyte Invasion By Antibodies That Target Plasmodium Falciparum Eba-175.
Plos Pathog. V. 9 03390 2013
PubMed-ID: 23717209  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003390

(-) Compounds

Molecule 1 - ERYTHROCYTE-BINDING ANTIGEN-175
    Chains: A, B
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Taxid: 4922
    Gene: EBA-175
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
 
Molecule 2 - ANTIBODY LIGHT CHAIN
    Chains: L, M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - ANTIBODY HEAVY CHAIN
    Chains: H, I
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHILM
Biological Unit 1 (1x): A H L 
Biological Unit 2 (1x):  B I M

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4QEX)

(-) Sites  (0, 0)

(no "Site" information available for 4QEX)

(-) SS Bonds  (31, 31)

Asymmetric Unit
No.Residues
1A:25 -A:36
2A:88 -A:166
3A:202 -A:215
4A:211 -A:283
5A:219 -A:281
6A:318 -A:353
7A:332 -A:344
8A:396 -A:471
9A:494 -A:574
10A:508 -A:518
11A:522 -A:595
12B:14 -B:45
13B:25 -B:36
14B:88 -B:166
15B:202 -B:215
16B:211 -B:283
17B:219 -B:281
18B:318 -B:353
19B:332 -B:344
20B:396 -B:471
21B:494 -B:574
22B:508 -B:518
23B:522 -B:595
24H:22 -H:92
25H:139 -H:194
26I:22 -I:92
27I:139 -I:194
28L:23 -L:88
29L:134 -L:194
30M:23 -M:88
31M:134 -M:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Asp L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:145 -Pro H:146
4Glu H:147 -Pro H:148
5Trp H:187 -Pro H:188
6Asp M:94 -Pro M:95
7Tyr M:140 -Pro M:141
8Phe I:145 -Pro I:146
9Glu I:147 -Pro I:148
10Trp I:187 -Pro I:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QEX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QEX)

(-) Exons   (0, 0)

(no "Exon" information available for 4QEX)

(-) 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:561
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee........eeeehhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhh.....hhhhhh..hhhhhhhh..............eee.........eeehhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qex A  17 KRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQITQWIKEWHGEFLLERDNRAKLPKSKCKNNALYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPYKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVECNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKCT 596
                                    26        36        46  ||    63        73        83        93       103       113       123     ||137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507||     525       535       545       555       565       575       585       595 
                                                           49|                                                                     129|                                                                                                                                                                                                                                                                                                                                                                                   508|                                                                               
                                                            57                                                                      134                                                                                                                                                                                                                                                                                                                                                                                    517                                                                               


Chain B from PDB  Type:PROTEIN  Length:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........eeee........eeeehhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhh.....hhhhhh..hhhhhhhh..............eee.........eeehhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qex B   8 NEVLSNCREKRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLAIIKTYKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQITQWIKEWHGEFLLERDNRAKLPKSKCKNNALYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPYKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVECNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKCT 596
                                    17        27        37        47       |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       438       448       458       468       478       488       498       508|      526       536       546       556       566       576       586       596
                                                                          55|                                                                                                                                                                                                                                                                                                                                                                                                                                                                508|                                                                               
                                                                           57                                                                                                                                                                                                                                                                                                                                                                                                                                                                 517                                                                               


Chain H from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee.....eeeeeeee........eeeeeee....eeeeeee......eee.......eeeeee....eeeeee........eeeeeee......ee...eeeee........eeeee...eeeeeeeeee.....eeee........eee...ee....eeeeeeeeehhhhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qex H   2 VQLQQSGPELVKPGTSVKISCKTSGYTFTENTMHWVKQSHGESLDWVGGINTDNGGTTYSQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCSTGYDAMDYWGQGTSVTVSSAKTTPPSVYPLNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 211
                                    11        21        31        41        51 |      60        70        80  |||   87        97       107       117     ||135       145       155       165       175       185       195       205      
                                                                             52A                            82A||                                      123|                                                                               
                                                                                                             82B|                                       132                                                                               
                                                                                                              82C                                                                                                                         


Chain I from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....eee.....eeeeeeee........eeeeeee....eeeeeee......eee.......eeeeee....eeeeee........eeeeeee......ee...eeeee........eeeee.......eeeeeeeeee.....eeee........eee...ee....eeeeeeeeehhhhh.....eeeee........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qex I   2 VQLQQSGPELVKPGTSVKISCKTSGYTFTENTMHWVKQSHGESLDWVGGINTDNGGTTYSQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCSTGYDAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 211
                                    11        21        31        41        51 |      60        70        80  |||   87        97       107       117       127|      141       151       161       171       181       191       201       211
                                                                             52A                            82A||                                          127|                                                                               
                                                                                                             82B|                                           132                                                                               
                                                                                                              82C                                                                                                                             


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eeeee....eeeeee.....ee..ee..eeeee......eeeee...ee.........ee....eeeeee...hhhhheeeeee............eeeeee......eeeee.........eeeeeeeeeee.....eeeeee..ee....eee...........eeeeeeeeeehhhhh....eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qex L   1 NIVLTQSPASLAVSLGQRATISCRASKGVDSYGNSFMHWYQQRPGQPPKLLIYLASHLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPFTFGSGTKLEIKRADAAPTVSIFPPSEQLTPGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKKGEFQHTGGR 209
                                    10        20        30||||    36        46        56        66        76        86        96       106       116   ||  127       137       147       157       167       177       187       197       207  
                                                        30A|||                                                                                       120|                                                                                       
                                                         30B||                                                                                        122                                                                                       
                                                          30C|                                                                                                                                                                                  
                                                           30D                                                                                                                                                                                  


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eeeee....eeeeee.....ee..ee..eeeee......eeeee...ee.........ee....eeeeee...hhhhheeeeee............eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...........eeeeeeeeeehhhhh....eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qex M   1 NIVLTQSPASLAVSLGQRATISCRASKGVDSYGNSFMHWYQQRPGQPPKLLIYLASHLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTPGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKKGEFQHTGGR 209
                                    10        20        30||||    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
                                                        30A|||                                                                                                                                                                                   
                                                         30B||                                                                                                                                                                                   
                                                          30C|                                                                                                                                                                                   
                                                           30D
   Legend:   → Mismatch (orange background)
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  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 4QEX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QEX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QEX)

(-) Gene Ontology  (3, 3)

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    Asp M:94 - Pro M:95   [ RasMol ]  
    Glu H:147 - Pro H:148   [ RasMol ]  
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4k2u CRYSTAL STRUCTURE OF PFEBA-175 F1 IN COMPLEX WITH R218 ANTIBODY FAB FRAGMENT