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(-) Description

Title :  STRUCTURE OF H5 AVIAN HAEMAGGLUTININ
 
Authors :  Y. Ha, D. J. Stevens, J. J. Skehel, D. C. Wiley
Date :  17 Aug 01  (Deposition) - 26 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Influenza, Receptor Complex, Fusion Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Ha, D. J. Stevens, J. J. Skehel, D. C. Wiley
H5 Avian And H9 Swine Influenza Virus Haemagglutinin Structures: Possible Origin Of Influenza Subtypes.
Embo J. V. 21 865 2002
PubMed-ID: 11867515  |  Reference-DOI: 10.1093/EMBOJ/21.5.865

(-) Compounds

Molecule 1 - HAEMAGGLUTININ (HA1 CHAIN)
    Chains: A
    Fragment: RESIDUES 1-325
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Other Details: AUTO CLEAVED FRAGMENT OF N-TERMINUS
    Strain: A/DUCK/SINGAPORE/3/97
 
Molecule 2 - HAEMAGGLUTININ (HA2 CHAIN)
    Chains: B
    Fragment: RESIDUES 1-176
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Other Details: AUTO CLEAVED FRAGMENT OF C-TERMINUS
    Strain: A/DUCK/SINGAPORE/3/97

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 21)
No.NameCountTypeFull Name
1NAG21Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:11BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWAREASN A:23BINDING SITE FOR RESIDUE NAG A 411
3AC3SOFTWAREASN A:165 , ASN A:236 , ASP A:237 , ALA A:238 , NAG A:413 , HOH A:642BINDING SITE FOR RESIDUE NAG A 412
4AC4SOFTWAREASN A:236 , NAG A:412BINDING SITE FOR RESIDUE NAG A 413
5AC5SOFTWAREASN A:275 , ASN A:286BINDING SITE FOR RESIDUE NAG A 431
6AC6SOFTWAREGLU B:150 , ASN B:154 , NAG B:178BINDING SITE FOR RESIDUE NAG B 177
7AC7SOFTWARENAG B:177BINDING SITE FOR RESIDUE NAG B 178

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -B:137
2A:42 -A:274
3A:55 -A:67
4A:90 -A:135
5A:278 -A:302
6B:144 -B:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JSM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JSM)

(-) 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:321
 aligned with A5Z226_I97A2 | A5Z226 from UniProtKB/TrEMBL  Length:564

    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 
         A5Z226_I97A2    17 DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCSLNGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKDNPVNGLCYPGDFNDYEELKHLLSSTNHFEKIRIIPRSSWSNHDASSGVSSACPYNGRSSFFRNVVWLIKKNNAYPTIKRSYNNTNQEDLLILWGIHHPNDAAEQTKLYQNPTTYVSVGTSTLNQRSVPEIATRPKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGGSAIMKSGLEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSGRLVLATGLRNVP 337
               SCOP domains d1jsma_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1jsmA02 A:1-47,A:270-321                       1jsmA01 A:48-269  [code=3.90.209.20, no name defined]                                                                                                                                                                         1jsmA02 A:1-47,A:270-321                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.....eeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeee........eee....eeeeee.eee..eee.....ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jsm A   1 DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKDNPVNGLCYPENFNDYEELKHLLSSTNHFEKIRIIPRSSWSNHDASSGVSSACPYNGRSSFFRNVVWLIKKNNAYPTIKRSYNNTNQEDLLILWGIHHPNDAAEQTKLYQNPTTYVSVGTSTLNQRSVPEIATRPKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGGSAIMKSGLEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSGRLVLATGLRNVP 321
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with A5Z226_I97A2 | A5Z226 from UniProtKB/TrEMBL  Length:564

    Alignment length:160
                                   352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
         A5Z226_I97A2   343 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGITNKVNSIIDKMNTQFEAVGKEFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYP 502
               SCOP domains d1jsmb_ B: Influenza hemagglutinin (stalk)                                                                                                                       SCOP domains
               CATH domains 1jsmB00 B:1-160  [code=3.90.20.10, no name defined]                                                                                                              CATH domains
           Pfam domains (1) Hemagglutinin-1jsmB01 B:1-160                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Hemagglutinin-1jsmB02 B:1-160                                                                                                                                    Pfam domains (2)
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jsm B   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGTTNKVNSIIDKMNTQFEAVGKEFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYP 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Hemagglutinin] (58)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A5Z226_I97A2 | A5Z226)
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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  A5Z226_I97A2 | A5Z226
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 Related Entries

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

UniProtKB/TrEMBL
        A5Z226_I97A2 | A5Z226: 1jsn 1jso

(-) Related Entries Specified in the PDB File

1jsd CRYSTAL STRUCTURE OF SWINE H9 HAEMAGGLUTININ
1jsh CRYSTAL STRUCTURE OF H9 HAEMAGGLUTININ COMPLEXED WITH LSTA RECEPTOR ANALOG
1jsi CRYSTAL STRUCTURE OF H9 HAEMAGGLUTININ BOUND TO LSTC RECEPTOR ANALOG
1jsn STRUCTURE OF AVIAN H5 HAEMAGGLUTININ COMPLEXED WITH LSTA RECEPTRO ANALOG
1jso STRUCTURE OF AVIAN H5 HAEMAGGLUTININ BOUND TO LSTC RECEPTOR ANALOG