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(-) Description

Title :  CRYSTAL STRUCTURE OF DENV1-E111 SINGLE CHAIN VARIABLE FRAGMENT BOUND TO DENV-1 DIII, STRAIN 16007.
 
Authors :  S. K. Austin, C. A. Nelson, D. H. Fremont, Center For Structural Geno Infectious Diseases (Csgid)
Date :  01 Jun 12  (Deposition) - 20 Jun 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Viral Envelope Proteins, Structural Genomics, Antibody Epitopes, Flavivirus, Dengue Virus, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, 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 - DENV1-E111 SINGLE CHAIN VARIABLE FRAGMENT (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAK400
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: IFN-ABR-/- C57BL/6 MICE
 
Molecule 2 - DENV1-E111 SINGLE CHAIN VARIABLE FRAGMENT (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAK400
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: IFN-ABR-/- C57BL/6 MICE
 
Molecule 3 - ENVELOPE GLYCOPROTEIN
    Chains: A
    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
    Gene: ENVELOPE DOMAIN III
    Organism Scientific: DENGUE VIRUS 1
    Organism Taxid: 11053
    Strain: 16007

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN L:37 , LYS L:45 , PRO L:59 , PHE L:62 , ASP L:81 , ASP L:82 , CL L:304BINDING SITE FOR RESIDUE GOL L 301
2AC2SOFTWARELYS L:39 , HOH L:455BINDING SITE FOR RESIDUE CL L 302
3AC3SOFTWARETYR H:95 , HOH L:412BINDING SITE FOR RESIDUE CL L 303
4AC4SOFTWAREARG L:61 , ASP L:81 , GOL L:301BINDING SITE FOR RESIDUE CL L 304
5AC5SOFTWAREGLU A:384 , TYR H:27 , THR H:28 , ASN H:31 , TRP H:32BINDING SITE FOR RESIDUE SO4 H 201
6AC6SOFTWAREASP H:73 , LYS H:74 , HOH H:336BINDING SITE FOR RESIDUE CL H 202

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:302 -A:333
2H:22 -H:96
3L:23 -L:88

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Asp L:94 -Pro L:95
3Phe H:101 -Pro H:102
4Ala A:331 -Pro A:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FFY)

(-) 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 A from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains d4ffya_ A: automated matches                                                                      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
                 4ffy A 299 YVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSTQDEKGATQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKG 395
                                   308       318       328       338       348       358       368       378       388       


Chain H from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d4ffyh_ H: automated matches                                                                                            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... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4ffy H   1 QVQLLQPGAELVKPGASMKLSCKASGYTFTNWWMHWVRLRPGRGLEWIGRIDPNSDVNKYNEKFENRASLTVDKHSSTAYMQLSSLTSEDSAIYYCARWFFPWYFDVWGTGTTVTVSSA 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain L from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains d4ffyl_ L: automated matches                                                                                     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. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4ffy L   1 NIVLTQSPASLAVSLGQRATISCRASESVDHYGNSFIYWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSETDFTLTIDSVETDDAATYYCQQNNEDPYTFGGGTKLEIKG 108
                                    10        20        30||||    36        46        56        66        76        86        96       106  
                                                        30A|||                                                                              
                                                         30B||                                                                              
                                                          30C|                                                                              
                                                           30D
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  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 4FFY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:331 - Pro A:332   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Phe H:101 - Pro H:102   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
 

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(-) Related Entries Specified in the PDB File

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