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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATITIS B VIRUS E-ANTIGEN
 
Authors :  M. A. Dimattia, N. R. Watts, S. J. Stahl, J. M. Grimes, A. C. Steven, D. I. S P. T. Wingfield
Date :  20 Dec 11  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.34
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  C,D,E  (1x)
Keywords :  Dimer Inversion, Four-Helix Bundle, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Dimattia, N. R. Watts, S. J. Stahl, J. M. Grimes, A. C. Steven, D. I. Stuart, P. T. Wingfield
Antigenic Switching Of Hepatitis B Virus By Alternative Dimerization Of The Capsid Protein.
Structure V. 21 133 2013
PubMed-ID: 23219881  |  Reference-DOI: 10.1016/J.STR.2012.10.017

(-) Compounds

Molecule 1 - FAB E6 HEAVY CHAIN
    Chains: A, C
    Fragment: FAB E6 HEAVY CHAIN
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FAB E6 LIGHT CHAIN
    Chains: B, D
    Fragment: FAB E6 LIGHT CHAIN
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - E-ANTIGEN
    Chains: E, F
    Engineered: YES
    Fragment: HBV E-ANTIGEN (CP(-10)149)
    Gene: PREC/C
    Mutation: YES
    Organism Common: HBV
    Organism Scientific: HEPATITIS B VIRUS
    Organism Taxid: 10407

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB   F
Biological Unit 2 (1x):   CDE 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3V6Z)

(-) Sites  (0, 0)

(no "Site" information available for 3V6Z)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:150 -A:205
3B:23 -B:94
4B:141 -B:201
5C:22 -C:96
6C:150 -C:205
7D:23 -D:94
8D:141 -D:201
9E:4 -E:71
10F:4 -F:71

(-) Cis Peptide Bonds  (18, 18)

Asymmetric Unit
No.Residues
1Phe A:156 -Pro A:157
2Glu A:158 -Ser A:159
3Trp A:198 -Pro A:199
4Ser B:7 -Pro B:8
5Ser B:82 -Ser B:83
6Tyr B:147 -Pro B:148
7Phe C:156 -Pro C:157
8Glu C:158 -Ser C:159
9Trp C:198 -Pro C:199
10Ser D:7 -Pro D:8
11Ser D:82 -Ser D:83
12Tyr D:147 -Pro D:148
13Glu E:53 -Ser E:54
14Pro E:55 -Glu E:56
15Asn E:100 -Thr E:101
16Glu F:53 -Ser F:54
17Pro F:55 -Glu F:56
18Asn F:100 -Thr F:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3V6Z)

(-) 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee.hhhh.....eeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee........eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6z A   1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGNYIYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTREGAYSGSSSYPMDYWGQGTSVTVSSAKTTPPSVYPLAPDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||143       153       163       173       183       193       203       213       223 
                                                                                                                                                                 136|                                                                                    
                                                                                                                                                                  140                                                                                    


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               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..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6z B   1 NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee.hhhh.....eeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee........eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6z C   1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGNYIYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTREGAYSGSSSYPMDYWGQGTSVTVSSAKTTPPSVYPLAPDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||143       153       163       173       183       193       203       213       223 
                                                                                                                                                                 136|                                                                                    
                                                                                                                                                                  140                                                                                    


Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               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..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6z D   1 NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain E from PDB  Type:PROTEIN  Length:148
 aligned with Q9QMH8_HBV | Q9QMH8 from UniProtKB/TrEMBL  Length:212

    Alignment length:148
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162        
           Q9QMH8_HBV    23 CLGWLWGMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGELMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILS 170
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6z E   4 CLGWLWGMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFAVWIRTPPAYRPPNAPILS 151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143        


Chain F from PDB  Type:PROTEIN  Length:148
 aligned with Q9QMH8_HBV | Q9QMH8 from UniProtKB/TrEMBL  Length:212

    Alignment length:148
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162        
           Q9QMH8_HBV    23 CLGWLWGMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGELMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILS 170
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6z F   4 CLGWLWGMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFAVWIRTPPAYRPPNAPILS 151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
   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 3V6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V6Z)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain E,F   (Q9QMH8_HBV | Q9QMH8)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  Cis Peptide Bonds
    Asn E:100 - Thr E:101   [ RasMol ]  
    Asn F:100 - Thr F:101   [ RasMol ]  
    Glu A:158 - Ser A:159   [ RasMol ]  
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    Ser B:82 - Ser B:83   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Ser D:82 - Ser D:83   [ RasMol ]  
    Trp A:198 - Pro A:199   [ RasMol ]  
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  3v6z
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  Q9QMH8_HBV | Q9QMH8
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 Related Entries

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(-) Related Entries Specified in the PDB File

3v6f CRYSTAL STRUCTURE OF FAB E6