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(-) Description

Title :  HAEMAGGLUTININ OF 2005 HUMAN H3N2 VIRUS
 
Authors :  X. Xiong, Y. P. Lin, S. A. Wharton, S. R. Martin, P. J. Coombs, S. G. Vachie E. Christodoulou, P. A. Walker, J. Liu, J. J. Skehel, S. J. Gamblin, A. J R. S. Daniels, J. W. Mccauley
Date :  29 Oct 12  (Deposition) - 07 Nov 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Viral Protein, Receptor Binding, Membrane Fusion, Influenza Virus Evolution, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. P. Lin, X. Xiong, S. A. Wharton, S. R. Martin, P. J. Coombs, S. G. Vachieri, E. Christodoulou, P. A. Walker, J. Liu, J. J. Skehel, S. J. Gamblin, A. J. Hay, R. S. Daniels, J. W. Mccauley
Evolution Of The Receptor Binding Properties Of The Influenza A(H3N2) Hemagglutinin.
Proc. Natl. Acad. Sci. Usa V. 109 21474 2012
PubMed-ID: 23236176  |  Reference-DOI: 10.1073/PNAS.1218841110

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PACGP67A
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-519
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: H3N2
    Synonym: HAEMAGGLUTININ
    Variant: A/HONG KONG/4443/2005

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
4TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE
Biological Unit 1 (4, 42)
No.NameCountTypeFull Name
1EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG30Ligand/IonN-ACETYL-D-GLUCOSAMINE
4TAM3Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:77 , GLN A:80 , ARG A:141 , SER A:146 , PHE A:147 , PHE A:148 , LEU A:151 , ARG A:255 , NAG A:804 , HOH A:2142BINDING SITE FOR RESIDUE EPE A1504
02AC2SOFTWARESER A:95 , PRO A:99 , TYR A:100 , ARG A:208 , ARG A:224 , GLU A:401BINDING SITE FOR RESIDUE EPE A1505
03AC3SOFTWAREARG A:383 , HOH A:2423BINDING SITE FOR RESIDUE TAM A1506
04AC4SOFTWAREASN A:38 , THR A:318 , LEU A:381BINDING SITE FOR MONO-SACCHARIDE NAG A 801 BOUND TO ASN A 38
05AC5SOFTWAREASN A:63 , TYR A:94 , HOH A:2421BINDING SITE FOR MONO-SACCHARIDE NAG A 802 BOUND TO ASN A 63
06AC6SOFTWAREASN A:126 , THR A:128BINDING SITE FOR MONO-SACCHARIDE NAG A 812 BOUND TO ASN A 126
07AC7SOFTWAREASN A:133 , EPE A:1504BINDING SITE FOR MONO-SACCHARIDE NAG A 804 BOUND TO ASN A 133
08AC8SOFTWAREASN A:165 , SER A:219 , PRO A:221 , ARG A:222 , NAG A:808 , HOH A:2169 , HOH A:2187 , HOH A:2211 , HOH A:2213BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 165 RESIDUES 805 TO 807
09AC9SOFTWAREALA A:163 , LEU A:164 , ASN A:165 , ARG A:201 , ASN A:246 , SER A:247 , THR A:248 , NAG A:805 , HOH A:2197BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 246 RESIDUES 808 TO 809
10BC1SOFTWAREASN A:285 , VAL A:297 , ASN A:298 , GLU A:398 , HOH A:2253 , HOH A:2267BINDING SITE FOR MONO-SACCHARIDE NAG A 811 BOUND TO ASN A 285
11BC2SOFTWAREASN A:483BINDING SITE FOR MONO-SACCHARIDE NAG A 813 BOUND TO ASN A 483

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:14 -A:466
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6A:473 -A:477

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:54 -Pro A:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YP7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YP7)

(-) Exons   (0, 0)

(no "Exon" information available for 2YP7)

(-) 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:490
 aligned with I2D7A8_9INFA | I2D7A8 from UniProtKB/TrEMBL  Length:566

    Alignment length:496
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513      
         I2D7A8_9INFA    24 NSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACKRKSNNSFFSRLNWLTHLKFKYPALNVTMPNNEKFDKLYIWGVHHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGIGQAADLKSTQAAINQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIK 519
               SCOP domains d2yp7a1 A:8-327 automated matches                                                                                                                                                                                                                                                                                               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......ee....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeee......eeee....eeeee..eee..eee.....ee......eeee.ee......eee..........------.................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yp7 A   8 NSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACKRKSNNSFFSRLNWLTHLKFKYPALNVTMPNNEKFDKLYIWGVHHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQ------AIAGFIENGWEGMVDGWYGFRHQNSEGIGQAADLKSTQAAINQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIK 503
                                    17        27        37        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       317       327      |337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497      
                                                                                                                                                                                                                                                                                                                                                         327    334
   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 2YP7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YP7)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (I2D7A8_9INFA | I2D7A8)
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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  2yp7
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 Related Entries

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

UniProtKB/TrEMBL
        I2D7A8_9INFA | I2D7A8: 2yp8 2yp9

(-) Related Entries Specified in the PDB File

2yp2 HAEMAGGLUTININ OF 2004 HUMAN H3N2 VIRUS
2yp3 HAEMAGGLUTININ OF 2004 HUMAN H3N2 VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6SLN
2yp4 HAEMAGGLUTININ OF 2004 HUMAN H3N2 VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE LSTC
2yp5 HAEMAGGLUTININ OF 2004 HUMAN H3N2 VIRUS IN COMPLEX
2yp7 HAEMAGGLUTININ OF 2005 HUMAN H3N2 VIRUS
2yp8 HAEMAGGLUTININ OF 2005 HUMAN H3N2 VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6SLN
2yp9 HAEMAGGLUTININ OF 2005 HUMAN H3N2 VIRUS IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3SLN
2ypg HAEMAGGLUTININ OF 1968 HUMAN H3N2 VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE LSTC