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(-) Description

Title :  THE HEMAGGLUTININ STRUCTURE OF AN AVIAN H1N1 INFLUENZA A VIRUS IN COMPLEX WITH LSTA
 
Authors :  G. Wang, A. Li, Q. Zhang, C. Wu, R. Zhang, Q. Cai, W. Song, K. -Y. Yuen
Date :  12 Jun 09  (Deposition) - 11 Aug 09  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Receptor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lin, G. Wang, A. Li, Q. Zhang, C. Wu, R. Zhang, Q. Cai, W. Song, K. -Y. Yuen
The Hemagglutinin Structure Of An Avian H1N1 Influenza A Virus
Virology V. 392 73 2009
PubMed-ID: 19628241  |  Reference-DOI: 10.1016/J.VIROL.2009.06.028

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A
    Fragment: HA1 CHAIN, UNP RESIDUES 15-338
    Organism Common: A/WDK/JX/12416/2005(H1N1)
    Organism Scientific: INFLUENZA A VIRUS (A/WDK/JX/12416/2005(H1N1))
    Organism Taxid: 666057
    Strain: WDK/JX/12416/2005
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B
    Organism Common: A/WDK/JX/12416/2005(H1N1)
    Organism Scientific: INFLUENZA A VIRUS (A/WDK/JX/12416/2005(H1N1))
    Organism Taxid: 666057
    Strain: WDK/JX/12416/2005

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (4, 21)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG6Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:68 , GLU A:70 , GLU A:90 , ASN A:91 , CYS A:94 , ARG A:224 , NDG A:627BINDING SITE FOR RESIDUE NDG A 626
2AC2SOFTWARENDG A:626BINDING SITE FOR RESIDUE NDG A 627
3AC3SOFTWAREASN A:15BINDING SITE FOR RESIDUE NAG A 631
4AC4SOFTWARETHR A:19 , ASN A:27 , HOH A:383BINDING SITE FOR RESIDUE NAG A 632
5AC5SOFTWARETYR A:95 , LYS A:133 , VAL A:135 , THR A:136 , ALA A:137 , TRP A:153 , HIS A:183 , GLU A:190 , LEU A:194 , GLN A:226 , HOH A:354 , GAL A:802BINDING SITE FOR RESIDUE SIA A 801
6AC6SOFTWAREGLU A:190 , GLN A:226 , HOH A:422 , SIA A:801 , NAG A:803BINDING SITE FOR RESIDUE GAL A 802
7AC7SOFTWAREGAL A:802BINDING SITE FOR RESIDUE NAG A 803

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:8 -B:637
2A:46 -A:278
3A:59 -A:71
4A:94 -A:139
5A:282 -A:306
6B:644 -B:648

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HTP)

(-) 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:324
 aligned with C7C6F1_9INFA | C7C6F1 from UniProtKB/TrEMBL  Length:563

    Alignment length:324
                                    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       334    
        C7C6F1_9INFA     15 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDNHNGKLCKLNGIAPLQLGKCNVAGWLLGNPECDLLLTANSWSYIIETSNSENGTCYPGEFIDYEELREQLSSVSSFERFEIFPKASSWPNHETTKGVTAACSYFGASSFYRNLLWITKKGTSYPKLSKSYTNNKGKEVLVLWGVHHPPTTSEQQTLYQNTDAYVSVGSSKYNRRFTPEIAARPKVRGQAGRMNYYWTLLDQGDTITFEATGNLIAPWYAFALNKGSDSGIITSDAPVHNCDTKCQTPHGAINSTLPFQNVHPITIGECPKYVKSTKLRMATGLRNIPSI  338
               SCOP domains d3htpa_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eeee.....eeee..hhhhhhhhhhhhhhhhh......eee...............hhhhhhhhh....eeeee..................eeeeee..eee....eee..........eeeeee......eeeeeeeee....hhhhhhhh.....eeee......ee...............eeeeeeeee....eeeeee...eeee..eeeee......eee....eeeeee.ee....ee.....ee......ee...ee......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3htp A    5 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDNHNGKLCKLNGIAPLQLGKCNVAGWLLGNPECDLLLTANSWSYIIETSNSENGTCYPGEFIDYEELREQLSSVSSFERFEIFPKASSWPNHETTKGVTAACSYFGASSFYRNLLWITKKGTSYPKLSKSYTNNKGKEVLVLWGVHHPPTTSEQQTLYQNTDAYVSVGSSKYNRRFTPEIAARPKVRGQAGRMNYYWTLLDQGDTITFEATGNLIAPWYAFALNKGSDSGIITSDAPVHNCDTKCQTPHGAINSTLPFQNVHPITIGECPKYVKSTKLRMATGLRNIPSI  327
                                    14        24        34        44        54        64        74        84        94       104       114       124       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    
                                                                                                                                                         132A                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with C7C6F1_9INFA | C7C6F1 from UniProtKB/TrEMBL  Length:563

    Alignment length:160
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
        C7C6F1_9INFA    342 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQFSGYAADQKSTQNAIDGITNKVNSIIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDVWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLRNNAKEIGNGCFEFYHKCDDECMESVKNGTYDYP  501
               SCOP domains d3htpb_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains 3htpB00 B:501-660  [code=3.90.20.10, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...eeee....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3htp B  501 GLFGAMAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSIIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDVWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLRNNAKEIGNGCFEFYHKCDDECMESVKNGTYDYP  660
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660
   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C7C6F1_9INFA | C7C6F1)
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/TrEMBL
        C7C6F1_9INFA | C7C6F1: 3hto 3htq 3htt

(-) Related Entries Specified in the PDB File

3hto HEMAGGLUTININ OF AVIAN H1N1 INFLUENZA A VIRUS
3htq HEMAGGLUTININ OF AVIAN H1N1 INFLUENZA A VIRUS IN COMPLEX WITH LSTC
3htt HEMAGGLUTININ OF AVIAN H1N1 INFLUENZA A VIRUS IN COMPLEX WITH 2,3-SIALYLLACTOSE