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(-) Description

Title :  CRYSTAL STRUCTURE OF DENV1-E111 FAB FRAGMENT BOUND TO DENV-1 DIII (WESTERN PACIFIC-74 STRAIN).
 
Authors :  S. K. Austin, C. A. Nelson, D. H. Fremont, Center For Structural Geno Infectious Diseases (Csgid)
Date :  01 Jun 12  (Deposition) - 27 Jun 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,H,L,X,Y,Z
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  X,Y,Z  (1x)
Keywords :  Structural Genomics, Antibody Fab Fragment, Flavivirus, Dengue Virus, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Immunoglobulin-Like Domain, Viral Envelope Protein, Virion, Immune System, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Austin, K. A. Dowd, B. Shrestha, C. A. Nelson, M. A. Edeling, S. Johnson, T. C. Pierson, M. S. Diamond, D. H. Fremont
Structural Basis Of Differential Neutralization Of Denv-1 Genotypes By An Antibody That Recognizes A Cryptic Epitope.
Plos Pathog. V. 8 02930 2012
PubMed-ID: 23055922  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002930

(-) Compounds

Molecule 1 - ENVELOPE PROTEIN E
    Chains: A, X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 573-679
    Organism Common: DENV-1
    Organism Scientific: DENGUE VIRUS 1
    Organism Taxid: 11059
    Strain: NAURU/WEST PAC/1974
 
Molecule 2 - DENV1-E111 FAB FRAGMENT (LIGHT CHAIN)
    Chains: L, Y
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - DENV1-E111 FAB FRAGMENT (HEAVY CHAIN)
    Chains: H, Z
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : AHLXYZ
Biological Unit 1 (1x): AHL   
Biological Unit 2 (1x):    XYZ

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4FFZ)

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:302 -A:333
2H:22 -H:92
3H:140 -H:195
4L:23 -L:88
5L:134 -L:194
6X:302 -X:333
7Y:23 -Y:88
8Z:22 -Z:92
9Z:140 -Z:195

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Ala A:331 -Pro A:332
2Ser L:7 -Pro L:8
3Asp L:94 -Pro L:95
4Tyr L:140 -Pro L:141
5Phe H:97 -Pro H:98
6Phe H:146 -Pro H:147
7Glu H:148 -Pro H:149
8Trp H:188 -Pro H:189
9Ala X:331 -Pro X:332
10Ser Y:7 -Pro Y:8
11Asp Y:94 -Pro Y:95
12Tyr Y:140 -Pro Y:141
13Phe Z:97 -Pro Z:98
14Phe Z:146 -Pro Z:147
15Glu Z:148 -Pro Z:149
16Trp Z:188 -Pro Z:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FFZ)

(-) 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:97
                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....ee.....eeeeeeee.....ee..eeee.........ee.....ee......eeeeee...eeeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                4ffz A  299 YVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKG  395
                                   308       318       328       338       348       358       368       378       388       


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee............eeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeee...........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ffz H    1 QVQLLQPGAELVKPGASMKLSCKASGYTFTNWWMHWVRLRPGRGLEWIGRIDPNSDVNKYNEKFENRASLTVDKHSSTAYMQLSSLTSEDSAIYYCARWFFPWYFDVWGTGTTVTVSSAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIES  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205       
                                                                              52A                            82A||               100A                                                                                                                
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C                                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               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....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ffz L    1 NIVLTQSPASLAVSLGQRATISCRASESVDHYGNSFIYWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSETDFTLTIDSVETDDAATYYCQQNNEDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20        30||||    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                        30A|||                                                                                                                                                                                      
                                                         30B||                                                                                                                                                                                      
                                                          30C|                                                                                                                                                                                      
                                                           30D                                                                                                                                                                                      


Chain X from PDB  Type:PROTEIN  Length:97
                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....ee.....eeeeeeee.....ee..eeee.........ee.....ee......eeeeee...eeeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                4ffz X  299 YVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKG  395
                                   308       318       328       338       348       358       368       378       388       


Chain Y from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ffz Y    1 NIVLTQSPASLAVSLGQRATISCRASESVDHYGNSFIYWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSETDFTLTIDSVETDDAATYYCQQNNEDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20        30||||    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                        30A|||                                                                                                                                                                                      
                                                         30B||                                                                                                                                                                                      
                                                          30C|                                                                                                                                                                                      
                                                           30D                                                                                                                                                                                      


Chain Z from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ffz Z    1 QVQLLQPGAELVKPGASMKLSCKASGYTFTNWWMHWVRLRPGRGLEWIGRIDPNSDVNKYNEKFENRASLTVDKHSSTAYMQLSSLTSEDSAIYYCARWFFPWYFDVWGTGTTVTVSSAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIES  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205       
                                                                              52A                            82A||               100A                                                                                                                
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C
   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 4FFZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 81)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:331 - Pro A:332   [ RasMol ]  
    Ala X:331 - Pro X:332   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Asp Y:94 - Pro Y:95   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
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    Trp H:188 - Pro H:189   [ RasMol ]  
    Trp Z:188 - Pro Z:189   [ RasMol ]  
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  POLG_DEN1W | P17763
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  Q88640_9FLAV | Q88640
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_DEN1W | P17763: 3l6p 3lkw 4al8 4gsx 4gt0 4lcy 4oig 5vic

(-) Related Entries Specified in the PDB File

3irc DENGUE-1 ENVELOPE PROTEIN DOMAIN III.
4ffz RELATED ID: IDP00272 RELATED DB: TARGETTRACK