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(-) Description

Title :  HUMAN H7N9 INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
 
Authors :  X. Xiong, L. F. Haire, S. R. Martin, S. A. Wharton, R. S. Daniels, M. S. Ben J. W. Mccauley, P. J. Collins, P. A. Walker, J. J. Skehel, S. J. Gamblin
Date :  10 Jun 13  (Deposition) - 03 Jul 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Viral Protein, H7N3, H7N9, H5N1, Fowl Plague Virus, Glycoprotein, Glycosylation, Virus Receptor, Bird Flu, Sialyllactosamine, 3Sln, 6Sln, Lstc, Pandemic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xiong, S. R. Martin, L. F. Haire, S. A. Wharton, R. S. Daniels, M. S. Bennett, J. W. Mccauley, P. J. Collins, P. A. Walker, J. J. Skehel, S. J. Gamblin
Receptor Binding By An H7N9 Influenza Virus From Humans
Nature V. 499 496 2013
PubMed-ID: 23787694  |  Reference-DOI: 10.1038/NATURE12372

(-) Compounds

Molecule 1 - HAEMAGGLUTININ HA1
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PACGP67A
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 19-339
    Organism Scientific: INFLUENZA VIRUS A/ANHUI/1/2013 (H7N9)
    Organism Taxid: 11320
    Other Details: WHO CHINESE NATIONAL INFLUENZA CENTER
 
Molecule 2 - HAEMAGGLUTININ HA2
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PACGP67A
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 340-516
    Organism Scientific: INFLUENZA VIRUS A/ANHUI/1/2013 (H7N9)
    Organism Taxid: 11320
    Other Details: WHO CHINESE NATIONAL INFLUENZA CENTER

 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, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA1Ligand/IonO-SIALIC ACID
4SO413Ligand/IonSULFATE ION
Biological Unit 1 (4, 63)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID
4SO439Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:117 , SER A:118 , GLY A:119 , ILE A:120 , ASN A:146BINDING SITE FOR RESIDUE SO4 A1323
02AC2SOFTWAREARG A:35 , ARG A:303 , HOH A:2078BINDING SITE FOR RESIDUE SO4 A1324
03AC3SOFTWAREGLN A:302 , ARG A:303 , SER A:304 , HOH A:2079BINDING SITE FOR RESIDUE SO4 A1325
04AC4SOFTWARETRP B:14 , GLU B:15 , GLY B:16 , ARG B:25BINDING SITE FOR RESIDUE SO4 B1173
05AC5SOFTWAREASN A:199 , ASN A:229 , ASN B:71 , GLU B:72BINDING SITE FOR RESIDUE SO4 B1174
06AC6SOFTWAREARG A:40BINDING SITE FOR RESIDUE SO4 A1326
07AC7SOFTWARESER A:84 , ASP A:85 , VAL A:86BINDING SITE FOR RESIDUE SO4 A1327
08AC8SOFTWAREARG A:163 , LYS A:164 , SER A:165BINDING SITE FOR RESIDUE SO4 A1328
09AC9SOFTWARELYS A:110 , GLU A:111 , ALA A:112 , ARG A:247BINDING SITE FOR RESIDUE SO4 A1329
10BC1SOFTWAREPHE A:92 , ASN A:94 , GLU A:95BINDING SITE FOR RESIDUE SO4 A1330
11BC2SOFTWARETHR A:20 , GLU A:21 , ARG A:22 , ASN B:53BINDING SITE FOR RESIDUE SO4 A1331
12BC3SOFTWAREGLN A:302 , HOH A:2071 , SER B:93 , TYR B:94BINDING SITE FOR RESIDUE SO4 B1175
13BC4SOFTWARELYS B:123 , GLU B:132BINDING SITE FOR RESIDUE SO4 B1176
14BC5SOFTWAREASN A:12 , GLY A:13BINDING SITE FOR MONO-SACCHARIDE NAG A1319 BOUND TO ASN A 12
15BC6SOFTWAREASN A:28 , ALA A:29 , THR A:30 , HOH A:2006 , HOH A:2077BINDING SITE FOR MONO-SACCHARIDE NAG A1317 BOUND TO ASN A 28
16BC7SOFTWAREASN A:231BINDING SITE FOR MONO-SACCHARIDE NAG A1318 BOUND TO ASN A 231
17BC8SOFTWAREARG A:291 , GLU B:72 , LYS B:75 , ASN B:79 , ASN B:82 , HOH B:2011 , HOH B:2025BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1171 THROUGH NAG B1172 BOUND TO ASN B 82
18BC9SOFTWARETYR A:88 , ALA A:125 , THR A:126 , SER A:127 , SER A:176 , VAL A:177 , LEU A:185 , GLN A:213 , GLY A:216BINDING SITE FOR POLY-SACCHARIDE RESIDUES SIA A1320 THROUGH NAG A1322

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -B:137
2A:42 -A:268
3A:54 -A:66
4A:87 -A:129
5A:272 -A:296
6B:144 -B:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BSF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BSF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BSF)

(-) Exons   (0, 0)

(no "Exon" information available for 4BSF)

(-) 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:317
 aligned with M4YV75_9INFA | M4YV75 from UniProtKB/TrEMBL  Length:560

    Alignment length:317
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       
         M4YV75_9INFA    19 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGISGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPEI 335
               SCOP domains d4bsfa_ A: automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee....eeeee..eee.ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..........eee.hhhhhhhhhhh...eeeee.............eeeee...ee....eee............eeeeee......eeeeeeeee..hhhhhhhhhh.....eeeee..eeeee...............eeeeeeeee....eeeeee...eeee.eeeee....eeee....ee......eee..ee......ee......eee..ee......eee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bsf A   1 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPEI 317
                                    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:170
 aligned with M4YV75_9INFA | M4YV75 from UniProtKB/TrEMBL  Length:560

    Alignment length:170
                                   349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509
         M4YV75_9INFA   340 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNR 509
               SCOP domains d4bsfb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee.....ee..hhhhhhhhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhh.......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bsf B   1 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNR 170
                                    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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BSF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BSF)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (M4YV75_9INFA | M4YV75)
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
        M4YV75_9INFA | M4YV75: 4bsa 4bsb 4bsc 4bsd 4bse

(-) Related Entries Specified in the PDB File

4bsa CRYSTAL STRUCTURE OF THE HAEMAGGLUTININ (WITH ASN-133 GLYCOSYLATION) FROM AN H7N9 INFLUENZA VIRUS ISOLATED FROM HUMANS
4bsb HUMAN H7N9 INFLUENZA VIRUS HAEMAGGLUTININ (WITH ASN-133 GLYCOSYLATION) IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE LSTC
4bsc HUMAN H7N9 INFLUENZA VIRUS HAEMAGGLUTININ (WITH ASN-133 GLYCOSYLATION) IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN
4bsd HUMAN H7N9 INFLUENZA VIRUS HAEMAGGLUTININ (WITH ASN-133 GLYCOSYLATION) IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
4bse HUMAN H7N9 INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE LSTC
4bsg CRYSTAL STRUCTURE OF AN H7N3 AVIAN INFLUENZA VIRUS HAEMAGGLUTININ
4bsh H7N3 AVIAN INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN
4bsi H7N3 AVIAN INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN