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(-) Description

Title :  STRUCTURAL BASIS OF ZIKA AND DENGUE VIRUS POTENT ANTIBODY CROSS-NEUTRALIZATION
 
Authors :  G. Barba-Spaeth
Date :  17 Jun 16  (Deposition) - 06 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immune System-Viral Protein Complex, Zika Virus, Broadly Neutralizing Antibody, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Barba-Spaeth, W. Dejnirattisai, A. Rouvinski, M. C. Vaney, I. Medits, A. Sharma, E. Simon-Loriere, A. Sakuntabhai, V. M. Cao-Lormeau, A. Haouz, P. England, K. Stiasny, J. Mongkolsapaya F. X. Heinz, G. R. Screaton, F. A. Rey
Structural Basis Of Potent Zika-Dengue Virus Antibody Cross-Neutralization.
Nature V. 536 48 2016
PubMed-ID: 27338953  |  Reference-DOI: 10.1038/NATURE18938
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENVELOPE PROTEIN E
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell: SCHNEIDER 2
    Expression System Common: FRUIT FLY
    Expression System Plasmid: PT389
    Expression System Taxid: 7227
    Expression System Vector Type: PMT-BIP-STREP
    Organism Common: ZIKV
    Organism Scientific: ZIKA VIRUS
    Organism Taxid: 64320
    Strain: MR 766

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NA1Ligand/IonSODIUM ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:158 , ASP B:161 , ARG B:164binding site for residue NA B 506
2AC2SOFTWAREGLN A:77 , GLY A:104 , GLY A:106 , GLU A:133 , LYS A:251 , HIS B:148 , GLY B:150 , MET B:151 , VAL B:153 , ASN B:154 , THR B:315 , LYS B:316 , ILE B:317binding site for Poly-Saccharide residues NAG B 501 through MAN B 505 bound to ASN B 154

(-) SS Bonds  (12, 12)

Asymmetric/Biological 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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:337 -Pro A:338
2Gly B:337 -Pro B:338

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LBV)

(-) 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 A from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...eeeeeee...eeeee......eeeeeeeeee....eeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeee.........eeeeeeeeeeeeeeeeeeee..hhh.eeeeeeeee....hhhhh.........eeeeee.....eeeee.hhh.eeeeeee.....eeeeee..eeeeeehhhhhh....eee......hhhh.eeeee.....eeeee...hhhhhhhhh...eeeeee..eee....eeeeeee.................eeeeeeeee.....eeeeeee......ee..eeee.......ee.ee.....ee......eeeeeeee...eeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lbv A   1 IRCIGVSNRDFVEGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGDLYYLTMNNKHWLVHKEWFHDIPLPWHAGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRS 403
                                    10   ||   23        33        43        53        63        73        83        93       103       113       123       133       143       155       165       175       185       195|      209       219       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403
                                        14|                                                                                                                                   152|                                     195|                         228|                                                                                                                                                                          
                                         18                                                                                                                                    155                                      200                          233                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee......eeeeeee...eeeee......eeeeeeeeee....eeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeee.........eeeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee....hhhhh...........eeeeee.....eeeee.hhh.eeeeeee....eeeeee..eeeeeehhhhhh....eee......hhhh.eeeee.....eeeee...hhhhhhhhh...eeeeee..eeee...eeeeeee...........ee....eeeeeeeee.....eeeeeee......ee..eeee.......ee.ee.....ee......eeeeeeee...eeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lbv B   1 IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGAPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRS 403
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 ||    205       215       225   ||  239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399    
                                                                                                                                                                                                                         192|                            229|                                                                                                                                                                         
                                                                                                                                                                                                                          198                             234
   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 5LBV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

UniProtKB/TrEMBL
        A0A024B7W1_Z | A0A024B7W1: 5goz 5gp1 5h30 5h32 5h37 5ire 5iz7 5jmt 5kqr 5kqs 5kve 5lbs 5lcv 5m5b 5mrk 5u4w 5uhy

(-) Related Entries Specified in the PDB File

5lbs 5LBS CONTAINS THE SAME PROTEIN COMPLEXED WITH SCFV FRAGMENT OF BROADLY NEUTRALIZED HUMAN ANTIBODY EDE1 C8
5lcv