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(-) Description

Title :  CRYSTAL STRUCTURE OF H5N1 INFLUENZA VIRUS HEMAGGLUTININ, STRAIN YU562 CRYSTAL FORM 2
 
Authors :  R. M. Dubois, H. Zaraket, M. Reddivari, R. J. Heath, S. W. White, C. J. Rus
Date :  14 May 11  (Deposition) - 14 Dec 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Hemagglutinin, Viral Protein, Viral Envelope Protein, Viral Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Dubois, H. Zaraket, M. Reddivari, R. J. Heath, S. W. White, C. J. Russell
Acid Stability Of The Hemagglutinin Protein Regulates H5N1 Influenza Virus Pathogenicity.
Plos Pathog. V. 7 02398 2011
PubMed-ID: 22144894  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002398

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PACGP67B
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 196426
    Strain: A/CHICKEN/HONG KONG/YU562/2001 (H5N1)
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PACGP67B
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 196426
    Strain: A/CHICKEN/HONG KONG/YU562/2001 (H5N1)

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO46Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:126 , TRP A:127 , SER A:128 , ASN A:129 , HIS A:130 , ARG A:166BINDING SITE FOR RESIDUE SO4 A 327
2AC2SOFTWARESER A:136 , SER A:137 , GLN A:226BINDING SITE FOR RESIDUE SO4 A 328
3AC3SOFTWAREASN A:169 , SER A:221 , ASN A:240 , ASP A:241 , ALA A:242 , NAG A:330BINDING SITE FOR RESIDUE NAG A 329
4AC4SOFTWAREASN A:240 , NAG A:329BINDING SITE FOR RESIDUE NAG A 330

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:52 -A:277
2A:64 -A:76
3A:97 -A:139
4A:281 -A:305

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S13)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S13)

(-) Exons   (0, 0)

(no "Exon" information available for 3S13)

(-) 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:277
 aligned with HEMA_I01A1 | Q80A30 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:277
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       
          HEMA_I01A1     38 LEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYLGKSSFFRNVVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPKIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSN  314
               SCOP domains d3s13a_ A: Hemagglutinin                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.ee...........ee......ee...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3s13 A   43 LEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYLGKSSFFRNVVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPKIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSN  312
                                    52 |      61        71        81 |      90      | 99       109       119      |127      |136       146       156       166       176       186       196       206       216       226       236       246       256       265       275       285       295       305       
                                     53A                           82A            96A                          125A|     133A                                                                                                                                264A                                                
                                                                                                                125B                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:43
 aligned with HEMA_I01A1 | Q80A30 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:43
                                   403       413       423       433   
          HEMA_I01A1    394 MNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVL  436
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                3s13 B   59 MNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVL  101
                                    68        78        88        98
   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)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S13)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HEMA_I01A1 | Q80A30)
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

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        HEMA_I01A1 | Q80A30: 3s12

(-) Related Entries Specified in the PDB File

3s11 3s12