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(-) Description

Title :  STRUCTURE OF THE BROADLY NEUTRALIZING ANTIBODY AP33 IN COMPLEX WITH ITS HCV EPITOPE (E2 RESIDUES 411-424)
 
Authors :  J. A. Potter, A. Owsianka, G. L Taylor, A. H. Patel
Date :  25 Jul 12  (Deposition) - 10 Oct 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Antibody Fab, Neutralizing Antibody, Hcv E2 Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Potter, A. M. Owsianka, N. Jeffery, D. J. Matthews, Z. Y. Keck, P. Lau, S. K. Foung, G. L. Taylor, A. H. Patel
Toward A Hepatitis C Virus Vaccine: The Structural Basis Of Hepatitis C Virus Neutralization By Ap33, A Broadly Neutralizing Antibody.
J. Virol. V. 86 12923 2012
PubMed-ID: 22993159  |  Reference-DOI: 10.1128/JVI.02052-12

(-) Compounds

Molecule 1 - NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - GENOME POLYPROTEIN
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 94-107
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4GAJ)

(-) Sites  (0, 0)

(no "Site" information available for 4GAJ)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Ser L:7 -Pro L:8
5Asp L:76 -Pro L:77
6Asp L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GAJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GAJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4GAJ)

(-) 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 H from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.....eeeeeee.....eeeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gaj H    1 EVQLQESGPSLVKPSQTLSLTCSVTGDTSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQLNSVTTEDTATYYCALITTTTYAMDYWGQGTSVTVSSAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP  212
                                    10        20      ||32        42        52        62        72        82|||     89        99 ||    107       117       133       143       153       163       173       183       193       203         
                                                     27|                                                  82A||               100A|                       126|                                                                               
                                                      30                                                   82B|                100B                        133                                                                               
                                                                                                            82C                                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee...........eeeeeeeeee......eeeee........eee...........eeeeeeeeehhhhhhh..eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gaj L    1 NIVLTQSPVSLAVSLGQRATISCRASESVDGYGNSFLHWFQQKPGQPPKLLIYLASNLNSGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNVDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206     
                                                     27A|||                                                                                                                                                                                        
                                                      27B||                                                                                                                                                                                        
                                                       27C|                                                                                                                                                                                        
                                                        27D                                                                                                                                                                                        


Chain P from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eee..eee. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                4gaj P  413 LINTNGSWHI  422
                                   422
   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 4GAJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GAJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GAJ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp L:76 - Pro L:77   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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(-) Related Entries Specified in the PDB File

4gag 4gay