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(-) Description

Title :  STRUCTURE OF THE HEPATITIS C VIRUS ENVELOPE GLYCOPROTEIN E2 ANTIGENIC REGION 412-423 BOUND TO THE BROADLY NEUTRALIZING ANTIBODY AP33
 
Authors :  L. Kong, I. A. Wilson, M. Law
Date :  18 Jul 12  (Deposition) - 26 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  B,C,D  (1x)
Biol. Unit 2:  A,H,L  (1x)
Keywords :  Immunoglobulin Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kong, E. Giang, T. Nieusma, J. B. Robbins, M. C. Deller, R. L. Stanfield, I. A. Wilson, M. Law
Structure Of Hepatitis C Virus Envelope Glycoprotein E2 Antigenic Site 412 To 423 In Complex With Antibody Ap33.
J. Virol. V. 86 13085 2012
PubMed-ID: 22973046  |  Reference-DOI: 10.1128/JVI.01939-12

(-) Compounds

Molecule 1 - E2 PEPTIDE
    Chains: B, A
    Engineered: YES
    Fragment: E2 PEPTIDE
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Other Details: THIS SEQUENCE NATURALLY OCCURS IN HEPATITIS C VIRUS
    Synthetic: YES
 
Molecule 2 - AP33 HEAVY CHAIN
    Chains: C, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Fragment: ANTIBODY FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - AP33 LIGHT CHAIN
    Chains: D, L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Fragment: ANTIBODY FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x):  BCD  
Biological Unit 2 (1x): A   HL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4G6A)

(-) Sites  (0, 0)

(no "Site" information available for 4G6A)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1C:22 -C:92
2C:140 -C:196
3C:216 -D:214
4D:23 -D:88
5D:134 -D:194
6H:22 -H:92
7H:140 -H:196
8H:216 -L:214
9L:23 -L:88
10L:134 -L:194

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Gly C:42 -Asn C:43
2Phe C:146 -Pro C:147
3Glu C:148 -Pro C:149
4Ser D:7 -Pro D:8
5Asp D:76 -Pro D:77
6Asp D:94 -Pro D:95
7Tyr D:140 -Pro D:141
8Phe H:146 -Pro H:147
9Glu H:148 -Pro H:149
10Ser L:7 -Pro L:8
11Asp L:76 -Pro L:77
12Asp L:94 -Pro L:95
13Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G6A)

(-) Exons   (0, 0)

(no "Exon" information available for 4G6A)

(-) 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:12
                                             
               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
                4g6a A  412 QLINTNGSWHIN  423
                                   421  


Chain B from PDB  Type:PROTEIN  Length:12
                                             
               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
                4g6a B  412 QLINTNGSWHIN  423
                                   421  


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               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........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g6a C    2 QLLEQSGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQLNSVTTEDTATYYCALITTTTYAMDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    11        21        31        41        51        61        71        81 |||    88        98  ||   106       116       126       136       146       156       166       176       186       196       206       216
                                                                                                           82A||               100A|                                                                                                                    
                                                                                                            82B|                100B                                                                                                                    
                                                                                                             82C                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g6a D    1 ELTLTQSPASLAVSLGQRATISCRASESVDGYGNSFLHWFQQKPGQPPKLLIYLASNLNSGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNVDPWTFGGGTKLEIKRAVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    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 H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g6a H    2 VQLLEQSGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQLNSVTTEDTATYYCALITTTTYAMDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                 |  10        20        30        40        50        60        70        80  |||   87        97   ||  105       115       125       135       145       155       165       175       185       195       205       215 
                                6A                                                                          82A||               100A|                                                                                                                    
                                                                                                             82B|                100B                                                                                                                    
                                                                                                              82C                                                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g6a L    1 ELTLTQSPASLAVSLGQRATISCRASESVDGYGNSFLHWFQQKPGQPPKLLIYLASNLNSGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNVDPWTFGGGTKLEIKRAVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    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
   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 4G6A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G6A)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp D:76 - Pro D:77   [ RasMol ]  
    Asp D:94 - Pro D:95   [ RasMol ]  
    Asp L:76 - Pro L:77   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Glu C:148 - Pro C:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly C:42 - Asn C:43   [ RasMol ]  
    Phe C:146 - Pro C:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr D:140 - Pro D:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9YK84_9HEPC | Q9YK84: 4dgv 4dgy
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        Q9YK84_9HEPC | Q9YK84: 4hs6 4hs8

(-) Related Entries Specified in the PDB File

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