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(-) Description

Title :  INFLUENZA VIRUS (VN1194) H5 HA WITH LSTC
 
Authors :  J. Liu, D. J. Stevens, S. J. Gamblin, J. J. Skehel
Date :  26 Feb 13  (Deposition) - 02 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  E,F
Biol. Unit 1:  E,F  (3x)
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Crusat, J. Liu, A. S. Palma, R. A. Childs, Y. Liu, S. A. Wharton, Y. P. Lin, P. J. Coombs, S. R. Martin, M. Matrosovich, Z. Chen, D. J. Stevens, V. M. Hien, T. T. Thanh, L. N. T. Nhu, L. A. Nguyet, D. Q. Ha, H. R. Van Doorn, T. T. Hien, H. S. Conradt, M. Kiso, S. J. Gamblin, W. Chai, J. J. Skehel, A. J. Hay, J. Farrar, M. D. De Jong, T. Feizi
Changes In The Hemagglutinin Of H5N1 Viruses During Human Infection - Influence On Receptor Binding.
Virology V. 447 326 2013
PubMed-ID: 24050651  |  Reference-DOI: 10.1016/J.VIROL.2013.08.010

(-) Compounds

Molecule 1 - HAEMAGGLUTININ
    Chains: E
    Engineered: YES
    Expression System: GALLUS GALLUS
    Expression System Common: CHICKEN
    Expression System Organ: EGG
    Expression System Taxid: 9031
    Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Other Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
    Strain: VIETNAM/1194/2004 (H5N1)
    Variant: VN/1194/04/NIBRG14 VACCINE STRAIN
 
Molecule 2 - HAEMAGGLUTININ
    Chains: F
    Engineered: YES
    Expression System: GALLUS GALLUS
    Expression System Common: CHICKEN
    Expression System Organ: EGG
    Expression System Taxid: 9031
    Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Other Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
    Strain: VIETNAM/1194/2004 (H5N1)
    Variant: VN/1194/04/NIBRG14 VACCINE STRAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : EF
Biological Unit 1 (3x): EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR E:95 , LEU E:133 , VAL E:135 , SER E:136 , SER E:137 , HIS E:183 , GLU E:190 , GLN E:226 , GLY E:228BINDING SITE FOR DI-SACCHARIDE GAL E1326 AND SIA E1327

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1E:8 -F:137
2E:46 -E:278
3E:59 -E:71
4E:94 -E:139
5E:282 -E:306
6F:144 -F:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZP1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZP1)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZP1)

(-) 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 E from PDB  Type:PROTEIN  Length:321
 aligned with Q6DQ34_9INFA | Q6DQ34 from UniProtKB/TrEMBL  Length:565

    Alignment length:321
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336 
         Q6DQ34_9INFA    17 DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP 337
               SCOP domains d3zp1e_ E: automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh....eeeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee.......eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp1 E   5 DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP 325
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324 


Chain F from PDB  Type:PROTEIN  Length:158
 aligned with Q6DQ34_9INFA | Q6DQ34 from UniProtKB/TrEMBL  Length:565

    Alignment length:158
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496        
         Q6DQ34_9INFA   347 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYD 504
               SCOP domains d3zp1f_ F: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zp1 F   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYD 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZP1)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain E,F   (Q6DQ34_9INFA | Q6DQ34)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
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:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    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:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the 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: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:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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: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
        Q6DQ34_9INFA | Q6DQ34: 2ibx
UniProtKB/TrEMBL
        Q6DQ34_9INFA | Q6DQ34: 3znk 3znl 3znm 3zp0 3zp2 3zp3 3zp6 3zpa 3zpb 4bgw 4bgx 4bgy 4cqp 4cqq 4cqr 4cqs 4cqu 4cqz 4cr0 5ajm 5jw4

(-) Related Entries Specified in the PDB File

3zp0 INFLUENZA VIRUS (VN1194) H5 HA WITH LSTA
3zp2 INFLUENZA VIRUS (VN1194) H5 HA A138V MUTANT WITH LSTA
3zp3 INFLUENZA VIRUS (VN1194) H5 HA A138V MUTANT WITH LSTC
3zp6 INFLUENZA VIRUS (VN1194) H5 E190D MUTANT HA WITH LSTC
3zpa INFLUENZA VIRUS (VN1194) H5 I155F MUTANT HA
3zpb INFLUENZA VIRUS (VN1194) H5 E190D MUTANT HA WITH LSTA