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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-ZIKA ANTIBODY Z004 BOUND TO DENV-1 ENVELOPE PROTEIN DIII
 
Authors :  J. R. Keeffe, A. P. West Jr. , H. B. Gristick, P. J. Bjorkman
Date :  14 Apr 17  (Deposition) - 03 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  E,H,L
Keywords :  Antibody, Fab, Zika, Dengue, Recurrent, Neutralizing, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. F. Robbiani, L. Bozzacco, J. R. Keeffe, R. Khouri, P. C. Olsen, A. Gazumyan, D. Schaefer-Babajew, S. Avila-Rios, L. Nogueira, R. Patel, S. A. Azzopardi, L. F. K. Uhl, M. Saeed, E. E. Sevilla-Reyes, M. Agudelo, K. H. Yao, J. Golijanin, H. B. Gristick, Y. E. Lee, A. Hurley M. Caskey, J. Pai, T. Oliveira, E. A. Wunder, G. Sacramento, N. Nery, C. Orge, F. Costa, M. G. Reis, N. M. Thomas, T. Eisenreich, D. M. Weinberger, A. R. P. De Almeida, A. P. West, C. M. Rice, P. J. Bjorkman, G. Reyes-Teran, A. I. Ko, M. R. Macdonald, M. C. Nussenzweig
Recurrent Potent Human Neutralizing Antibodies To Zika Viru In Brazil And Mexico.
Cell V. 169 597 2017
PubMed-ID: 28475892  |  Reference-DOI: 10.1016/J.CELL.2017.04.024

(-) Compounds

Molecule 1 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293-6E
    Expression System Common: HUMAN
    Expression System Plasmid: PTT5
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293-6E
    Expression System Common: HUMAN
    Expression System Plasmid: PTT5
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IMMUNOGLOBULIN KAPPA LIGHT CHAIN EU
 
Molecule 3 - DENGUE 1 ENVELOPE DIII DOMAIN
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: DENV-1
    Organism Scientific: DENGUE VIRUS TYPE 1 (STRAIN NAURU/WEST PAC/1974)
    Organism Taxid: 11059
    Strain: NAURU/WEST PAC/1974

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : EHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5VIC)

(-) Sites  (0, 0)

(no "Site" information available for 5VIC)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1E:302 -E:333
2H:22 -H:92
3H:140 -H:196
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Ser L:7 -Pro L:8
3Val L:94 -Pro L:95
4Tyr L:140 -Pro L:141
5Ala E:331 -Pro E:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VIC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VIC)

(-) Exons   (0, 0)

(no "Exon" information available for 5VIC)

(-) 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 E from PDB  Type:PROTEIN  Length:83
                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee.....eeeeeeee.....ee..eeee..ee.....ee......eeeeee...eeeee.hhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                5vic E  298 SYVMCTGSFKLEKEVAEGTVLVQVKYEGTDAPCKIPFSSQNGRLITANPIVTDKEKPVNIEAEPPESYIVVGAGEKALKLSWF  392
                                   307      |320       330       340|      357       367    || 379       389   
                                          314|                   340|                     372|                 
                                           318                    348                      375                 


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee...hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee.........eeeeeeee.....eeee........eee...ee.....eeeeeee...hhhhh....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vic H    1 EVQLLESGGGLVQPGGSLRLTCATSGFTFRDYAMSWVRQAPGKGLEWVSSYSGIDDSTYYADSVKGRFTISRDNSKSTLSLHMNSLRAEDSALYFCAKDRGPRGVGELFDSWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121      |135       145       155       165       175       185       195       205         
                                                                              52A                            82A||               100A||||                         128|                                                                                 
                                                                                                              82B|                100B|||                          133                                                                                 
                                                                                                               82C                 100C||                                                                                                              
                                                                                                                                    100D|                                                                                                              
                                                                                                                                     100E                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....ee............eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vic L    1 DIQMTQSPSTLSASVGDRVTITCRASQSISKWLAWYQQKPGKAPKLLIYTTSTLKSGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHFYSVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 5VIC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VIC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VIC)

(-) Gene Ontology  (64, 64)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Sites
(no "Sites" information available for 5vic)
 
  Cis Peptide Bonds
    Ala E:331 - Pro E:332   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Val L:94 - Pro L:95   [ RasMol ]  
 

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  5vic
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  POLG_DEN1W | P17763
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  S6B291_HUMAN | S6B291
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGK_HUMAN | P0DOX7: 4nm4 4nm8 5vig
        POLG_DEN1W | P17763: 3l6p 3lkw 4al8 4ffz 4gsx 4gt0 4lcy 4oig
        S6B291_HUMAN | S6B291: 3mnw 3mnz 4eow 5c7k 5cus 5d9q 5veb 5vig 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        S6B291_HUMAN | S6B291: 4llw 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

5vig