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(-) Description

Title :  THEORETICAL MODEL OF H4 INFLUENZA VIRUS
 
Authors :  O. Spiga, A. Bernini, A. Ciutti, S. Chiellini, F. Prischi, V. Venditti, N. Niccolai
Date :  27 Dec 05  (Deposition) - 17 Jan 06  (Release) - 17 Jan 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D,E,F
Keywords :  Trimer, Influenza Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Spiga, A. Bernini, A. Ciutti, S. Chiellini, F. Prischi, V. Venditti, N. Niccolai
Structurally Driven Selection Of Hemagglutinin Antigenic Fragments From Influenza Viruses
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: A, C, E
    Organism Scientific: INFLUENZA A VIRUS
    Strain: A/DUCK/ALBERTA/28/76 H4N6
 
Molecule 2 - HEMAGGLUTININ HA2
    Chains: B, D, F
    Organism Scientific: INFLUENZA A VIRUS
    Strain: A/DUCK/ALBERTA/28/76 H4N6

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2FHV)

(-) Sites  (0, 0)

(no "Site" information available for 2FHV)

(-) SS Bonds  (18, 18)

Theoretical Model
No.Residues
1A:2 -B:137
2A:40 -A:267
3A:52 -A:64
4A:85 -A:127
5A:271 -A:295
6B:144 -B:148
7C:2 -D:137
8C:40 -C:267
9C:52 -C:64
10C:85 -C:127
11C:271 -C:295
12D:144 -D:148
13E:2 -F:137
14E:40 -E:267
15E:52 -E:64
16E:85 -E:127
17E:271 -E:295
18F:144 -F:148

(-) Cis Peptide Bonds  (3, 3)

Theoretical Model
No.Residues
1Ser A:42 -Pro A:43
2Ser C:42 -Pro C:43
3Ser E:42 -Pro E:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FHV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FHV)

(-) Exons   (0, 0)

(no "Exon" information available for 2FHV)

(-) Sequences/Alignments

Theoretical Model
   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:319
 aligned with HEMA_I76A1 | P03443 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:319
                                    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         
           HEMA_I76A1    25 ICLGHHAVSNGTMVKTLTDDQVEVVTAQELVESQHLPELCPSPLRLVDGQTCDIVNGALGSPGCDHLNGAEWDVFIERPTAVDTCYPFDVPDYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVNDFFNRLNWLTKSDGDAYPLQNLTKVNNGDYARLYIWGVHHPSTDTEQTNLYKNNPGRVTVSTKTSQTSVVPNIGSRPWVRGQSGRISFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNSQKKSTILNTAVPIGSCVSKCHTDRGSISTTKPFQNISRISIRDCPKYVKQGSLKLATGMRNIPEKATR 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eee.......eee..eee.ee.............eee....hhhhhhhh...hhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.............eeeeee..eee....eee...........eeeeee......eeeeeeeee..hhhhhhhhhh....eeeeee...eeee...............eeeeeeeee....eeeeeeee.eeee.eeee.......eeee...........eee..eee.....ee.....eeee..ee......eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fhv A   1 ICLGHHAVSNGTMVKTLTDDQVEVVTAQELVESQHLPELCPSPLRLVDGQTCDIVNGALGSPGCDHLNGAEWDVFIERPTAVDTCYPFDVPDYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVNDFFNRLNWLTKSDGDAYPLQNLTKVNNGDYARLYIWGVHHPSTDTEQTNLYKNNPGRVTVSTKTSQTSVVPNIGSRPWVRGQSGRISFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNSQKKSTILNTAVPIGSCVSKCHTDRGSISTTKPFQNISRISIRDCPKYVKQGSLKLATGMRNIPEKATR 319
                                    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         


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with HEMA_I76A1 | P03443 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:173
                                   353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513   
           HEMA_I76A1   344 GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAEFLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGCFEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQI 516
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee....hhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fhv B   1 GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAEFLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGCFEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQI 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain C from PDB  Type:PROTEIN  Length:319
 aligned with HEMA_I76A1 | P03443 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:319
                                    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         
           HEMA_I76A1    25 ICLGHHAVSNGTMVKTLTDDQVEVVTAQELVESQHLPELCPSPLRLVDGQTCDIVNGALGSPGCDHLNGAEWDVFIERPTAVDTCYPFDVPDYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVNDFFNRLNWLTKSDGDAYPLQNLTKVNNGDYARLYIWGVHHPSTDTEQTNLYKNNPGRVTVSTKTSQTSVVPNIGSRPWVRGQSGRISFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNSQKKSTILNTAVPIGSCVSKCHTDRGSISTTKPFQNISRISIRDCPKYVKQGSLKLATGMRNIPEKATR 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eee.......eee..eee.ee.............eee....hhhhhhhh...hhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.............eeeeee..eee....eee...........eeeeee......eeeeeeeee..hhhhhhhhhh....eeeeee...eeee...............eeeeeeeee....eeeeeeee.eeee.eeee.......eeee...........eee..eee.....ee.....eeee..ee......eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fhv C   1 ICLGHHAVSNGTMVKTLTDDQVEVVTAQELVESQHLPELCPSPLRLVDGQTCDIVNGALGSPGCDHLNGAEWDVFIERPTAVDTCYPFDVPDYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVNDFFNRLNWLTKSDGDAYPLQNLTKVNNGDYARLYIWGVHHPSTDTEQTNLYKNNPGRVTVSTKTSQTSVVPNIGSRPWVRGQSGRISFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNSQKKSTILNTAVPIGSCVSKCHTDRGSISTTKPFQNISRISIRDCPKYVKQGSLKLATGMRNIPEKATR 319
                                    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         


Chain D from PDB  Type:PROTEIN  Length:173
 aligned with HEMA_I76A1 | P03443 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:173
                                   353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513   
           HEMA_I76A1   344 GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAEFLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGCFEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQI 516
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee....hhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fhv D   1 GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAEFLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGCFEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQI 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain E from PDB  Type:PROTEIN  Length:319
 aligned with HEMA_I76A1 | P03443 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:319
                                    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         
           HEMA_I76A1    25 ICLGHHAVSNGTMVKTLTDDQVEVVTAQELVESQHLPELCPSPLRLVDGQTCDIVNGALGSPGCDHLNGAEWDVFIERPTAVDTCYPFDVPDYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVNDFFNRLNWLTKSDGDAYPLQNLTKVNNGDYARLYIWGVHHPSTDTEQTNLYKNNPGRVTVSTKTSQTSVVPNIGSRPWVRGQSGRISFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNSQKKSTILNTAVPIGSCVSKCHTDRGSISTTKPFQNISRISIRDCPKYVKQGSLKLATGMRNIPEKATR 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eee.......eee..eee.ee.............eee....hhhhhhhh...hhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.............eeeeee..eee....eee...........eeeeee......eeeeeeeee..hhhhhhhhhh....eeeeee...eeee...............eeeeeeeee....eeeeeeee.eeee.eeee.......eeee...........eee..eee.....ee.....eeee..ee......eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fhv E   1 ICLGHHAVSNGTMVKTLTDDQVEVVTAQELVESQHLPELCPSPLRLVDGQTCDIVNGALGSPGCDHLNGAEWDVFIERPTAVDTCYPFDVPDYQSLRSILANNGKFEFIAEEFQWNTVKQNGKSGACKRANVNDFFNRLNWLTKSDGDAYPLQNLTKVNNGDYARLYIWGVHHPSTDTEQTNLYKNNPGRVTVSTKTSQTSVVPNIGSRPWVRGQSGRISFYWTIVEPGDLIVFNTIGNLIAPRGHYKLNSQKKSTILNTAVPIGSCVSKCHTDRGSISTTKPFQNISRISIRDCPKYVKQGSLKLATGMRNIPEKATR 319
                                    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         


Chain F from PDB  Type:PROTEIN  Length:173
 aligned with HEMA_I76A1 | P03443 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:173
                                   353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513   
           HEMA_I76A1   344 GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAEFLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGCFEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQI 516
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee....hhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fhv F   1 GLFGAIAGFIENGWQGLIDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRIQDLEKYVEDTKIDLWSYNAEFLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGCFEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQI 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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  (0, 0)

(no "SCOP Domain" information available for 2FHV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FHV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FHV)

(-) Gene Ontology  (17, 17)

Theoretical Model(hide GO term definitions)
Chain A,B,C,D,E,F   (HEMA_I76A1 | P03443)
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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    Ser A:42 - Pro A:43   [ RasMol ]  
    Ser C:42 - Pro C:43   [ RasMol ]  
    Ser E:42 - Pro E:43   [ RasMol ]  
 

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  2fhv
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  HEMA_I76A1 | P03443
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 Related Entries

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

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