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(-) Description

Title :  SOLUTION STRUCTURES OF THE ENVELOPE PROTEIN DOMAIN III FROM THE DENGUE-2 VIRUS
 
Authors :  K. Huang, J. Cheng
Date :  03 Jul 07  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Domain Iii, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. C. Huang, M. C. Lee, C. W. Wu, K. J. Huang, H. Y. Lei, J. W. Cheng
Solution Structure And Neutralizing Antibody Binding Studie Of Domain Iii Of The Dengue-2 Virus Envelope Protein.
Proteins V. 70 1116 2008
PubMed-ID: 18004779  |  Reference-DOI: 10.1002/PROT.21806

(-) Compounds

Molecule 1 - DOMAIN III OF ENVELOPE PROTEIN E
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-BLUE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 469-577
    Organism Scientific: DENGUE VIRUS
    Organism Taxid: 11060
    Strain: 2

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2JSF)

(-) Sites  (0, 0)

(no "Site" information available for 2JSF)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:14 -A:45

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JSF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JSF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JSF)

(-) Exons   (0, 0)

(no "Exon" information available for 2JSF)

(-) Sequences/Alignments

NMR Structure
   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:117
 aligned with POLG_DEN2U | P18356 from UniProtKB/Swiss-Prot  Length:679

    Alignment length:117
                                   478       488       498       508       518       528       538       548       558       568       578       
           POLG_DEN2U   469 MDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETT 585
               SCOP domains d2jsfa_ A: automated matches                                                                                          SCOP domains
               CATH domains 2jsfA00 A:1-117  [code=2.60.40.350, no name defined]                                                                  CATH domains
               Pfam domains Flavi_gl-Flavi_glycop_C-2jsfA01 A:10-105                                                                 ------------ Pfam domains
         Sec.struct. author ................eeeeeeeeee.....eeeeeeee.....ee..ee..hhhhh....ee.....ee......eeeeee...eeeeeee......eeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2jsf A   1 MDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSLEHHHHHH 117
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: no clan defined [family: Flavi_glycop_C] (15)
(-)
Clan: no clan defined [family: Flavi_glycoprot] (10)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (POLG_DEN2U | P18356)
molecular function
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    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.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
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.
    GO:0044165    host cell endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0044167    host cell endoplasmic reticulum membrane    The lipid bilayer surrounding the host cell endoplasmic reticulum.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_DEN2U | P18356: 2r69 2r6p 3c6r 3ixy 3iya

(-) Related Entries Specified in the PDB File

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