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(-) Description

Title :  INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY
 
Authors :  T. Bizebard, D. Fleury, B. Gigant, S. A. Wharton, J. J. Skehel, M. Knossow
Date :  22 Dec 97  (Deposition) - 29 Apr 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Complex (Hemagglutinin/Immmunoglobulin), Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fleury, S. A. Wharton, J. J. Skehel, M. Knossow, T. Bizebard
Antigen Distortion Allows Influenza Virus To Escape Neutralization.
Nat. Struct. Biol. V. 5 119 1998
PubMed-ID: 9461077  |  Reference-DOI: 10.1038/NSB0298-119
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN (IGG1, LAMBDA)
    Cell: HYBRIDOMA
    Chains: A
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - IMMUNOGLOBULIN (IGG1, LAMBDA)
    Cell: HYBRIDOMA
    Chains: B
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB-C
 
Molecule 3 - HEMAGGLUTININ
    Chains: C
    Engineered: YES
    Fragment: PROTEOLYTIC FRAGMENT "HA TOP" CONTAINING HA1 RESIDUES 28 - 328
    Organism Scientific: INFLUENZA A VIRUS (A/X-31(H3N2))
    Organism Taxid: 132504
    Other Details: A REASSORTANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
    Strain: X31

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:203 , THR A:204 , HIS C:56 , GLU C:280BINDING SITE FOR RESIDUE ZN C 1
2AC2SOFTWAREGLU A:16 , ASP A:154 , HIS A:191BINDING SITE FOR RESIDUE ZN A 211
3AC3SOFTWAREASP A:141 , HIS B:173BINDING SITE FOR RESIDUE ZN A 212

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:90
2A:137 -A:196
3B:22 -B:95
4B:149 -B:204
5C:52 -C:277
6C:64 -C:76
7C:97 -C:139
8C:281 -C:305

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr A:143 -Pro A:144
2Phe B:155 -Pro B:156
3Glu B:157 -Pro B:158
4Trp B:197 -Pro B:198
5Asn C:54 -Pro C:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VIR)

(-) Sequences/Alignments

Asymmetric/Biological 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:210
                                                                                                                                                                                                                                                  
               SCOP domains d2vira1 A:1-110 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d2vira2 A:111-210 Immunoglobulin light chain lambda constant domain, CL-lambda                       SCOP domains
               CATH domains 2virA01 A:1-110 Immunoglobulins                                                                               2virA02 A:111-210 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...eeeeee........hhh..eeeeee...eeeeee.............eeeeee..eeeeeee...hhh..eeeeeee....eee....eeeee...............hhhhh...eeeeeeeeee.....eeeeee........eee..........eeeeeeeee.hhhhh....eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vir A   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLS 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:223
                                                                                                                                    126  127                                                                                                               
                                    29        39        49        59        69        79        89        99       109       119      |  - |     135       145       155       165       175       185       195       205       215       225       235   
         Q99LC4_MOUSE    20 QVQLQQSGAELARPGASVRLSCKASGYTFTGYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCARSSYYSYDLF----AYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 238
               SCOP domains d2virb1 B:1-120 Immunoglobulin heavy chain variable do main, VH                                                           d2virb2 B:121-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2virB01 B:1-123 Immunoglobulins                                                                                              2virB02 B:124-221 Immunoglobulins                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeeeee.......eeeeeee.....eeeeeee...-..eee...hhh.eeeeee....eeeeeee...hhh.eeeeeee-eeee....eeee......eee..........eeeee..........eeeeeeeee.......eeeehhh...........eee..eeeeeeeeeee.........eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vir B   1 QVQLKESGPGLVAPSQSLSITCTVSGFLLISNGVHWVRQPPGKGLEWLGVIWAG-GNTNYNSALMSRVSISKDNSKSQVFLKMKSLQTDDTAMYYCAR-DFYDYDVFYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 221
                                    10        20        30        40        50   | |  59        69        79        89       |98       108       118       128       138       148       158       168       178       188       198       208       218   
                                                                                54 |                                        97 |                                                                                                                           
                                                                                  55                                          98                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:267
 aligned with HEMA_I68A0 | P03437 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:267
                                    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       
           HEMA_I68A0    59 VQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYV 325
               SCOP domains d2virc_ C: Hemagglutinin                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2virC01       2virC02 C:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                   2virC01 C:43-56,C:273-309             CATH domains
               Pfam domains Hemagglutinin-2virC01 C:43-309                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author .......eee.....eee.....hhhhhh..hhhhhh......eeee...............hhhhhhhhhhh....eee..............hhh...........eee...........eeeeee.....eeeeeeeee...hhhhhhhh......eeee.....eee...............eeeeeeeee...eeeeeee....eee.eee.......eeee...eee.................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vir C  43 VQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQDETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLDVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPDGSIPNDKPFQNVNKITYGACPKYV 309
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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  (5, 5)

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

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Hemagglutinin] (58)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (Q99LC4_MOUSE | Q99LC4)

Chain C   (HEMA_I68A0 | P03437)
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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  2vir
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  HEMA_I68A0 | P03437
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  Q99LC4_MOUSE | Q99LC4
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMA_I68A0 | P03437: 1eo8 1fyt 1ha0 1hgd 1hge 1hgf 1hgg 1hgh 1hgi 1hgj 1htm 1j8h 1ken 1kg0 1pyw 1qfu 1qu1 2hmg 2vis 2vit 2viu 2ypg 3eym 3hmg 3s4s 3s5l 3vun 3ztj 4c56 4hmg 5hmg
        Q99LC4_MOUSE | Q99LC4: 1afv 3hkf
UniProtKB/TrEMBL
        Q99LC4_MOUSE | Q99LC4: 1ae6 1e6j 1f58 1gig 1jhk 1jnl 1jnn 2a1w 2ntf 2vis 2vit 4q0x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2VIR)