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(-) Description

Title :  STRUCTURE OF THE HEPATITIS C VIRUS STRAIN J4 GLYCOPROTEIN E2 ANTIGENIC REGION 532-540 BOUND TO THE FAB FRAGMENT OF THE NON-NEUTRALIZING ANTIBODY DAO5
 
Authors :  I. Vasiliauskaite, F. A. Rey, T. Krey
Date :  16 Apr 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Envelope Glycoprotein, Hepatitis C Virus, Fab Fragment, Cd81 Binding Loop, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Vasiliauskaite, A. Owsianka, P. England, A. G. Khan, S. Cole, D. Bankwitz, S. K. H. Foung, T. Pietschmann, J. Marcotrigiano, F. A. Rey, A. H. Patel, T. Krey
Conformational Flexibility In The Immunoglobulin-Like Domai Of The Hepatitis C Virus Glycoprotein E2.
Mbio V. 8 2017
PubMed-ID: 28512091  |  Reference-DOI: 10.1128/MBIO.00382-17

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A
    Engineered: YES
    Fragment: UNP RESIDUES 529-540
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Synthetic: YES
 
Molecule 2 - HEAVY CHAIN OF FAB FRAGMENT DERIVED FROM NON-NEUTRALIZING ANTIBODY DAO5
    Chains: H
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER 2
    Expression System Common: FRUIT FLY
    Expression System Plasmid: PMT-FAB-STREP
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - LIGHT CHAIN OF FAB FRAGMENT DERIVED FROM NON-NEUTRALIZING ANTIBODY DAO5
    Chains: L
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER 2
    Expression System Common: FRUIT FLY
    Expression System Plasmid: PMT-FAB-STREP
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5NPH)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:147 -H:202
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly H:42 -Pro H:43
2Tyr H:103 -Pro H:104
3Phe H:153 -Pro H:154
4Glu H:155 -Pro H:156
5Trp H:195 -Pro H:196
6Ser L:7 -Pro L:8
7Trp L:94 -Pro L:95
8Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NPH)

(-) 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:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5nph A 532 NETDVMLLN 540


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee.....eeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nph H   1 EVQLQQSGPELVKPGASLKISCKTSGYTFTDFTFHWVKLSHGPSLEWIGTIKPSNGDTAYNQKFKGKATLSVDKSASTAHIEFRSLTSEDSAVYFCARFGGSYPYAMDYWGQGTSVIVSSAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   146       156       166       176       186       196       206       216    
                                                                                                                                                              133|                                                                                
                                                                                                                                                               140                                                                                


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee....eeeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nph L   0 SDIVLTQSPATLSVTPGDRVSLSCRASQGIYNYVHWFQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVESEDFGMYFCQQTNKWPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   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 5NPH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (79, 79)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 5nph)
 
  Cis Peptide Bonds
    Glu H:155 - Pro H:156   [ RasMol ]  
    Gly H:42 - Pro H:43   [ RasMol ]  
    Phe H:153 - Pro H:154   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:195 - Pro H:196   [ RasMol ]  
    Trp L:94 - Pro L:95   [ RasMol ]  
    Tyr H:103 - Pro H:104   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  5nph
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  POLG_HCVJ4 | O92972
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HCVJ4 | O92972: 1nb4 1nb6 1nb7 2f55 2mts 2xhu 2xhv 2xhw 2yoj 3cso 3gnv 3gnw 3gol 3hky 3lkh 3mwv 3mww 3ska 3ske 3skh 3tyq 3tyv 3u4o 3u4r 3uph 3upi 4dru 4eaw 4gmc 4iz0 4j02 4j04 4j06 4j08 4j0a 4jjs 4jju 4jtw 4jty 4jtz 4ju1 4ju2 4ju3 4ju4 4ju6 4ju7 4jvq 4jy0 4jy1 4mz4 4oow 4ry4 4ry5 4ry6 4ry7 5czb

(-) Related Entries Specified in the PDB File

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