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(-) Description

Title :  WEST NILE VIRUS ENVELOPE PROTEIN DIII IN COMPLEX WITH NEUTRALIZING E16 ANTIBODY FAB
 
Authors :  G. E. Nybakken, T. Oliphant, M. S. Diamond, D. H. Fremont
Date :  27 May 05  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  E,H,L
Keywords :  Antibody, Fab, Neutralizing, Virus, Envelope, Viral Protein/Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. E. Nybakken, T. Oliphant, S. Johnson, S. Burke, M. S. Diamond, D. H. Fremont
Structural Basis Of West Nile Virus Neutralization By A Therapeutic Antibody.
Nature V. 437 764 2005
PubMed-ID: 16193056  |  Reference-DOI: 10.1038/NATURE03956
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENVELOPE PROTEIN
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAIN III (RESIDUES 463-568)
    Organism Scientific: WEST NILE VIRUS
    Organism Taxid: 11082
 
Molecule 2 - HEAVY CHAIN OF E16 ANTIBODY
    Chains: H
    Fragment: VH AND CH1 DOMAINS
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - LIGHT CHAIN OF E16 ANTIBODY
    Chains: L
    Fragment: VL AND CL DOMAINS
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: THE HEAVY CHAIN AND LIGHT CHAIN WERE MADE FROM A MOUSE HYBRIDOMA

 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 1ZTX)

(-) Sites  (0, 0)

(no "Site" information available for 1ZTX)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1E:305 -E:336
2H:22 -H:92
3H:142 -H:208
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly E:334 -Pro E:335
2Phe H:148 -Pro H:149
3Trp H:199 -Pro H:200
4Thr L:94 -Pro L:95
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZTX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZTX)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZTX)

(-) 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:101
 aligned with Q91KZ4_WNV | Q91KZ4 from UniProtKB/TrEMBL  Length:296

    Alignment length:101
                                   200       210       220       230       240       250       260       270       280       290 
          Q91KZ4_WNV    191 TTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKS  291
               SCOP domains d1ztxe_ E: automated matches                                                                          SCOP domains
               CATH domains 1ztxE00 E:300-400  [code=2.60.40.350, no name defined]                                                CATH domains
               Pfam domains -Flavi_glycop_C-1ztxE01 E:301-399                                                                   - Pfam domains
         Sec.struct. author .........eeeeeeeee.....eeeeeee......ee..eeeeee..eeee..ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                1ztx E  300 TTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKS  400
                                   309       319       329       339       349       359       369       379       389       399 


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains -----------------------------------------------------------------------------------------------------------------------d1ztxh1 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1ztxH01 H:1-113 Immunoglobulins                                                                                        1ztxH02 H:114-228 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhh.eeeeeee......eeeeeee.....eee......eeeeeee....eeeeeee..hhhhheeeeeeee......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeeee......eeeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ztx H    1 QVQLQQSGSELMKPGASVQISCKATGYTFSDYWIEWVKQRPGHGLEWIGDILCGTGRTRYNEKLKAMATFTADTSSNTAFMQLSSLTSEDSAVYYCARSASYGDYADYWGHGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124     ||136       146       157|      172       184       194 || || 206|      217     ||  
                                                                              52A                            82A||               100A|                           130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                100B                            133                   156||     171       183           198 ||  208             226  
                                                                                                               82C                                                                       157|                               200|                       
                                                                                                                                                                                          162                                202                       


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d1ztxl1 L:1-107 automated matches                                                                          d1ztxl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains 1ztxL01 L:1-108 Immunoglobulins                                                                             1ztxL02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ztx L    1 DIVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLISWASTRHTGVPDRFTGSGSGTDYTLTISSVQAEDLALYYCQQHYTTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    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  (4, 4)

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

(-) CATH Domains  (2, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Flavi_glycop_C] (15)

(-) Gene Ontology  (38, 40)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (Q91KZ4_WNV | Q91KZ4)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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: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: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:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
    Gly E:334 - Pro E:335   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Thr L:94 - Pro L:95   [ RasMol ]  
    Trp H:199 - Pro H:200   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  Q91KZ4_WNV | Q91KZ4
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGG2B_MOUSE | P01867: 1cbv 1cf8 1cic 1etz 1fj1 1fl3 1hq4 1mam 1nbv 1osp 1ub5 1ub6 1ynk 1ynl 2gjz 2gk0 2q8a 2q8b 2rgs 3cfd 3cfe

(-) Related Entries Specified in the PDB File

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