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(-) Description

Title :  CRYSTAL STRUCTURE OF DENV1-E106 FAB BOUND TO DENV-1 ENVELOPE PROTEIN DIII
 
Authors :  M. A. Edeling, C. A. Nelson, D. H. Fremont, Center For Structural Gen Infectious Diseases (Csgid)
Date :  11 Jun 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  E,H,L
Keywords :  Antibody, Fab, Neutralizing, Virus, Envelope, Viral Protein, Immune System, Antibody Epitope, Infectious Disease, Center For Structural Genomics Of Infectious Diseases (Csgid), Niaid, National Institute Of Allergy And Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Edeling, S. K. Austin, B. Shrestha, K. A. Dowd, S. Mukherjee, C. A. Nelson, S. Johnson, M. N. Mabila, E. A. Christian, J. Rucker, T. C. Pierson, M. S. Diamond, D. H. Fremont
Crystal Structure Of Denv1-E106 Fab Bound To Denv-1 Envelop Protein Diii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEAVY CHAIN OF E106 ANTIBODY (VH AND CH1 OF IGG2C)
    Chains: H
    Fragment: VH AND CH1 DOMAINS
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: IFN-ABR-/- C57BL/6 MICE
 
Molecule 2 - ENVELOPE PROTEIN
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21(A)+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DOMAIN III (UNP RESIDUES 293-399)
    Gene: E
    Organism Scientific: DENGUE VIRUS 1
    Organism Taxid: 11053
    Strain: 16007
 
Molecule 3 - LIGHT CHAIN OF E106 ANTIBODY (KAPPA)
    Chains: L
    Fragment: VL AND CL DOMAINS
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: IFN-ABR-/- C57BL/6 MICE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : EHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4L5F)

(-) Sites  (0, 0)

(no "Site" information available for 4L5F)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1E:302 -E:333
2H:22 -H:92
3H:140 -H:195
4L:23 -L:88
5L: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
4Ala E:331 -Pro E:332
5Ser L:7 -Pro L:8
6Leu 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 4L5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L5F)

(-) Exons   (0, 0)

(no "Exon" information available for 4L5F)

(-) 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 E from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4l5fe_ E: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....ee.....eeeeeeee.....ee..eeee................ee......eeeee......eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4l5f E 297 MSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSTQDEKGATQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKK 394
                                   306       316       326       336       346       356       366       376       386        


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eee.....eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5f H   1 EVQLQQSGPELVKPGASVKISCKASGYSFIGYYIHWVKQSPEKSLEWIGEINPRTGDTTYNQKFKAKATLTVDKSSSTAYMQLTSLTSEDSAVYYCTKRINWALDYWGQGTTLTVSSAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIESRR 214
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206        
                                                                              52A                            82A||                                                                                                                                    
                                                                                                              82B|                                                                                                                                    
                                                                                                               82C                                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4l5fl1 L:1-107 automated matches                                                                          d4l5fl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5f L   1 ETTVTQSPASLSVATGEKVTIRCITSTDIDDDMNWYQQKPGERPKLLISEGNTLRPGVPSRFSSSGYGTDFVFTIENTLSEDVADYFCLQSDNLPLTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L5F)

(-) Gene Ontology  (17, 17)

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 4l5f)
 
  Cis Peptide Bonds
    Ala E:331 - Pro E:332   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Leu L:94 - Pro L:95   [ 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

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