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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-ZIKA ANTIBODY Z006 BOUND TO ZIKA VIRUS ENVELOPE PROTEIN DIII
 
Authors :  J. R. Keeffe, A. P. West Jr. , H. B. Gristick, P. J. Bjorkman
Date :  16 Apr 17  (Deposition) - 03 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,G,H,L,Z
Biol. Unit 1:  H,L,Z  (1x)
Biol. Unit 2:  A,B,G  (1x)
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, A
    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, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB LIGHT CHAIN
    Chains: L, B
    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, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IMMUNOGLOBULIN KAPPA LIGHT CHAIN EU
 
Molecule 3 - ZIKA VIRUS ENVELOPE PROTEIN DIII
    Chains: Z, G
    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: ZIKV
    Organism Scientific: ZIKA VIRUS
    Organism Taxid: 64320
    Strain: MR 766

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABGHLZ
Biological Unit 1 (1x):    HLZ
Biological Unit 2 (1x): ABG   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:94 , HIS G:398 , HIS G:399binding site for residue FLC A 500

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:134 -B:194
4G:308 -G:339
5H:22 -H:92
6H:140 -H:196
7L:134 -L:194
8Z:308 -Z:339

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Tyr L:140 -Pro L:141
5Gly Z:337 -Pro Z:338
6Phe A:146 -Pro A:147
7Glu A:148 -Pro A:149
8Ser B:7 -Pro B:8
9Tyr B:140 -Pro B:141
10Gly G:337 -Pro G:338

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VIG)

(-) 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:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee......eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee.hhhhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vig A    2 VQLLESGGGLVQPGGSLRLSCAASGFTFKNYAMAWVRQAPGKGLEWVSLLYNSEESTYYADSVKGRFTISRDNSKNTLFLQMNRLRVEDTAVYFCVRDRSNGWSSINLWGRGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||| 104       114       124  ||   140       150       160       170       180       190       200       210   
                                                                             52A                            82A||               100A||                        127|                                                                               
                                                                                                             82B|                100B|                         134                                                                               
                                                                                                              82C                 100C                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeeee.......eeee..hhhhhh..eeeeeeeeeee....eeeeeee........eeeee.........eeeeeeeeeehhhhhh...eeeeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vig B    1 DIQMTQSPSTLSASVGDRVTMTCRASQTISGWLAWYQQKPGKAPKLLIYQASRLESGIPSRFSGSGSGTEFTLTISSLQPDDVATYYCQQYSTFWTFGLGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90   ||  101       111       121       131       141       151       161       171       181       191       201       211  
                                                                                                                        94|                                                                                                                     
                                                                                                                         96                                                                                                                     


Chain G from PDB  Type:PROTEIN  Length:100
                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.....eeeeeee......ee..eeee..........ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                5vig G  305 YSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSG  404
                                   314       324       334       344       354       364       374       384       394       404


Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee......eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee.hhhhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vig H    2 VQLLESGGGLVQPGGSLRLSCAASGFTFKNYAMAWVRQAPGKGLEWVSLLYNSEESTYYADSVKGRFTISRDNSKNTLFLQMNRLRVEDTAVYFCVRDRSNGWSSINLWGRGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||| 104       114       124  ||   140       150       160       170       180       190       200       210   
                                                                             52A                            82A||               100A||                        127|                                                                               
                                                                                                             82B|                100B|                         134                                                                               
                                                                                                              82C                 100C                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeeee.......eeee..hhhhhh..eeeeeeeeeee....eeeeeee........eeeee.........eeeeeeeeeehhhhhh...eeeeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vig L    1 DIQMTQSPSTLSASVGDRVTMTCRASQTISGWLAWYQQKPGKAPKLLIYQASRLESGIPSRFSGSGSGTEFTLTISSLQPDDVATYYCQQYSTFWTFGLGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90   ||  101       111       121       131       141       151       161       171       181       191       201       211  
                                                                                                                        94|                                                                                                                     
                                                                                                                         96                                                                                                                     


Chain Z from PDB  Type:PROTEIN  Length:100
                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.....eeeeeee......ee..eeee..........ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                5vig Z  305 YSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSG  404
                                   314       324       334       344       354       364       374       384       394       404
   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 5VIG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5VIG)

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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 5vic
        S6B291_HUMAN | S6B291: 3mnw 3mnz 4eow 5c7k 5cus 5d9q 5veb 5vic 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        S6B291_HUMAN | S6B291: 4llw 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

5vic