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(-) Description

Title :  STRUCTURE OF NEUTRALIZING ANTIBODY BOUND TO ZIKA ENVELOPE PROTEIN
 
Authors :  Q. Wang, H. Yang, X. Liu, L. Dai, T. Ma, J. Qi, G. Wong, R. Peng, S. Liu, J. Li J. Song, J. Liu, J. He, H. Yuan, Y. Xiong, Y. Liao, J. Li, J. Yang, Z. Tong, B. Griffin, Y. Bi, M. Liang, X. Xu, G. Cheng, P. Wang, X. Qiu, G. Kobinger J. Yan, G. F. Gao
Date :  29 Sep 16  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  A (2x),H (1x),L (1x)
Biol. Unit 2:  B (2x),C (1x),D (1x)
Keywords :  Zika Virus, Human Neutralizing Antibodies, Envelope Protein, Molecular Determinants, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Wang, H. Yang, X. Liu, L. Dai, T. Ma, J. Qi, G. Wong, R. Peng, S. Liu, J. Li, S. Li, J. Song, J. Liu, J. He, H. Yuan, Y. Xiong, Y. Liao, J. Li, J. Yang, Z. Tong, B. D. Griffin, Y. Bi, M. Liang, X. Xu, C. Qin, G. Cheng, X. Zhang, P. Wang, X. Qiu, G. Kobinger, Y. Shi, J. Yan, G. F. Gao
Molecular Determinants Of Human Neutralizing Antibodies Isolated From A Patient Infected With Zika Virus
Sci Transl Med V. 8 Ra179 2016
PubMed-ID: 27974667  |  Reference-DOI: 10.1126/SCITRANSLMED.AAI8336

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ENVELOPE PROTEIN, UNP RESIDUES 291-699
    Organism Common: ZIKV
    Organism Scientific: ZIKA VIRUS
    Organism Taxid: 64320
    Strain: MR 766
 
Molecule 2 - ANTIBODY HEAVY CHAIN
    Chains: H, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY LIGHT CHAIN
    Chains: L, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (2x): A (2x)   H (1x)L (1x)
Biological Unit 2 (2x):  B (2x)C (1x)D (1x)  

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5GZO)

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:3 -A:30
2A:60 -A:121
3A:74 -A:105
4A:92 -A:116
5A:190 -A:291
6A:308 -A:339
7B:3 -B:30
8B:60 -B:121
9B:74 -B:105
10B:92 -B:116
11B:190 -B:291
12B:308 -B:339
13C:22 -C:96
14C:146 -C:202
15D:23 -D:88
16D:134 -D:194
17H:22 -H:96
18H:146 -H:202
19L:23 -L:88
20L:134 -L:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:337 -Pro A:338
2Phe H:152 -Pro H:153
3Glu H:154 -Pro H:155
4Ser L:7 -Pro L:8
5Tyr L:94 -Pro L:95
6Tyr L:140 -Pro L:141
7Gly B:337 -Pro B:338
8Phe C:152 -Pro C:153
9Glu C:154 -Pro C:155
10Ser D:7 -Pro D:8
11Tyr D:94 -Pro D:95
12Tyr D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GZO)

(-) 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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee......eeeeeee..eeeeee......eeeeeeeeee...eeeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeeehhhhh....eeeeeeeeeeeeeeeeeeeee.....eeeeeeeee.....eeeeee.....eeeee.hhh.eeeeeee.........eeeeee..eeeeeehhhhhhh...ee...........hhhh.eeee.......eeee...hhhhhhhhh...eeeeee..eeee...eeeeeee.................eee....ee.....eeeeeee......ee..eeee..........ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gzo A   1 IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGS 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||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
                                                                                                                                                                           146|                                                                                                                                                                                                                                                   
                                                                                                                                                                            162                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.......eeeeee..eeeeee......eeeeeeeeee...eeeeeeeeeeeeeeeeeee.........hhhhh...eeee..eeeehhhhh....eeeeeeeeeeeeeeeeeeeee.....eeeeeeeee.....eeeeee.....eeeee.hhh.eeeeeee.........eeeeee..eeeeeehhhhhh....ee...........hhhh.eeee.......eeee...hhhhhhhhh...eeeeee..eeee...eeeeeee.................eeeeeeeee.....eeeeeee......ee..eeee..........ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gzo B   1 IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGS 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||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
                                                                                                                                                                           146|                                                                                                                                                                                                                                                   
                                                                                                                                                                            162                                                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee.....eeeeeeeeeee....eeeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gzo C   1 QVQLQESGPGLVKPSGTLSLTCAVSGGSISSSNWWSWVRQPPGKGLEWIGEIYHSGSTNYNPSLKSRVTISVDKSKNQFSLKLSSVTAADTAVYYCARDRDDLSPFDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185       195       205       215    
                                                                                                                                                               134|                                                                               
                                                                                                                                                                140                                                                               


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gzo D   1 DIVMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSYPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gzo H   1 QVQLQESGPGLVKPSGTLSLTCAVSGGSISSSNWWSWVRQPPGKGLEWIGEIYHSGSTNYNPSLKSRVTISVDKSKNQFSLKLSSVTAADTAVYYCARDRDDLSPFDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185       195       205       215    
                                                                                                                                                               134|                                                                               
                                                                                                                                                                140                                                                               


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gzo L   1 DIVMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSYPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    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 5GZO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5gzo)
 
  Cis Peptide Bonds
    Glu C:154 - Pro C:155   [ RasMol ]  
    Glu H:154 - Pro H:155   [ RasMol ]  
    Gly A:337 - Pro A:338   [ RasMol ]  
    Gly B:337 - Pro B:338   [ RasMol ]  
    Phe C:152 - Pro C:153   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr D:140 - Pro D:141   [ RasMol ]  
    Tyr D:94 - Pro D:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
 
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  5gzo
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  A0A1B0XTC8_Z | A0A1B0XTC8
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  H9A910_ZIKV | H9A910
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 Related Entries

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

UniProtKB/Swiss-Prot
        H9A910_ZIKV | H9A910: 5goz 5gp1 5gxj 5gzn 5kqr 5kqs 5m5b
UniProtKB/TrEMBL
        A0A1B0XTC8_Z | A0A1B0XTC8: 5gzn 5gzr

(-) Related Entries Specified in the PDB File

5gzn