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(-) Description

Title :  HAEMAGGLUTININ FROM A TRANSMISSIBLE MUTANT H5 INFLUENZA VIRUS IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
 
Authors :  X. Xiong, P. J. Coombs, S. R Martin, J. Liu, H. Xiao, J. W. Mccauley, K. Lo P. A. Walker, P. J. Collins, Y. Kawaoka, J. J. Skehel, S. J. Gamblin
Date :  29 Mar 13  (Deposition) - 24 Apr 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Viral Protein, N-Glycosylation, Virus Receptor, Bird Flu (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xiong, P. J. Coombs, S. R Martin, J. Liu, H. Xiao, J. W. Mccauley, K. Locher, P. A. Walker, P. J. Collins, Y. Kawaoka, J. J. Skehel, S. J. Gamblin
Receptor Binding By A Ferret-Transmissible H5 Avian Influenza Virus
Nature V. 497 392 2013
PubMed-ID: 23615615  |  Reference-DOI: 10.1038/NATURE12144

(-) 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: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
    Organism Scientific: INFLUENZA VIRUS
    Organism Taxid: 284218
    Other Details: DESCRIBED BY M. IMAI ET AL. NATURE (2012)
    Strain: A/VIET NAM/1203/2004(H5N1)
    Synonym: HAEMAGGLUTININ HA1
    Variant: TRANSMISSIBLE MUTANT
 
Molecule 2 - HEMAGGLUTININ
    Chains: B
    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: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 343-509
    Organism Scientific: INFLUENZA VIRUS
    Organism Taxid: 284218
    Other Details: DESCRIBED BY M. IMAI ET AL. NATURE (2012)
    Strain: A/VIET NAM/1203/2004(H5N1)
    Synonym: HAEMAGGLUTININ HA2
    Variant: TRANSMISSIBLE MUTANT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3FUC1Ligand/IonALPHA-L-FUCOSE
4GAL1Ligand/IonBETA-D-GALACTOSE
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (7, 36)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3FUC3Ligand/IonALPHA-L-FUCOSE
4GAL3Ligand/IonBETA-D-GALACTOSE
5MAN3Ligand/IonALPHA-D-MANNOSE
6NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:4 , TRP B:14 , HIS B:25 , ASN B:135 , HOH B:2149BINDING SITE FOR RESIDUE EPE B1168
2AC2SOFTWAREASN A:11 , HOH A:2017BINDING SITE FOR MONO-SACCHARIDE NAG A1323 BOUND TO ASN A 11
3AC3SOFTWAREASN A:23 , GLN A:169 , HOH A:2238 , HOH A:2239BINDING SITE FOR MONO-SACCHARIDE NAG A1324 BOUND TO ASN A 23
4AC4SOFTWAREGLU A:21 , VAL A:24 , THR A:25 , ASN A:165 , SER A:217 , ASN A:236 , ASP A:237 , ALA A:238 , ARG A:318 , ASN A:319 , PRO A:321 , HOH A:2026 , HOH A:2034 , HOH A:2036 , HOH A:2182 , HOH A:2240 , HOH A:2241 , HOH A:2243 , HOH A:2245 , GLU B:11 , GLY B:12BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1325 THROUGH FUC A1330 BOUND TO ASN A 165
5AC5SOFTWARETYR A:91 , LEU A:129 , VAL A:131 , SER A:132 , SER A:133 , HIS A:179 , GLU A:186 , LEU A:190 , GLY A:221 , HOH A:2091 , HOH A:2132 , HOH A:2134 , HOH A:2246BINDING SITE FOR POLY-SACCHARIDE RESIDUES SIA A1331 THROUGH NAG A1333

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -B:137
2A:42 -A:274
3A:55 -A:67
4A:90 -A:135
5A:278 -A:302
6B:144 -B:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BH4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BH4)

(-) Exons   (0, 0)

(no "Exon" information available for 4BH4)

(-) 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 Q5EP31_9INFA | Q5EP31 from UniProtKB/TrEMBL  Length:568

    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    
         Q5EP31_9INFA    15 KSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQ 338
               SCOP domains d4bh4a_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhh...............eee...........eee.hhhhhhhhhh...eeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee......eee....eeeeee.eee..eee.....ee......eee..ee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bh4 A  -1 DPDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLAIGLRNSPQ 322
                                     8        18        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    


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with Q5EP31_9INFA | Q5EP31 from UniProtKB/TrEMBL  Length:568

    Alignment length:167
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       
         Q5EP31_9INFA   347 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEAR 513
               SCOP domains d4bh4b_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bh4 B   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEAR 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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 4BH4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BH4)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5EP31_9INFA | Q5EP31)
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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  4bh4
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  Q5EP31_9INFA | Q5EP31
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 Related Entries

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

UniProtKB/TrEMBL
        Q5EP31_9INFA | Q5EP31: 4bh2 4bh3 4n5z

(-) Related Entries Specified in the PDB File

4bgw STRUCTURE OF H5 (VN1194) INFLUENZA HAEMAGGLUTININ
4bgx H5 (VN1194) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN
4bgy H5 (VN1194) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
4bgz CRYSTAL STRUCTURE OF H5 (TYTY) INFLUENZA VIRUS HAEMAGGLUTININ
4bh0 H5 (TYTY) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN
4bh1 H5 (TYTY) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
4bh2 CRYSTAL STRUCTURE OF THE HAEMAGGLUTININ FROM A TRANSMISSIBLE MUTANT H5 INFLUENZA VIRUS
4bh3 HAEMAGGLUTININ FROM A TRANSMISSIBLE MUTANT H5 INFLUENZA VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN