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(-) Description

Title :  INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY
 
Authors :  D. Fleury, B. Gigant, R. S. Daniels, J. J. Skehel, M. Knossow, T. Bizebar
Date :  22 Mar 00  (Deposition) - 12 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (3x)
Keywords :  Complex (Hemagglutinin-Immmunoglobulin), Hemagglutinin, Immunoglobulin, Viral Protein, Immune System Complex, Viral Protein- Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fleury, R. S. Daniels, J. J. Skehel, M. Knossow, T. Bizebard
Structural Evidence For Recognition Of A Single Epitope By Two Distinct Antibodies.
Proteins V. 40 572 2000 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMAGGLUTININ (HA1 CHAIN)
    Chains: A
    Fragment: BROMELAIN RELEASED FRAGMENT
    Organism Scientific: INFLUENZA A VIRUS (A/X-31(H3N2))
    Organism Taxid: 132504
    Other Details: A RECOMBINANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
    Strain: X31
 
Molecule 2 - HEMAGGLUTININ (HA2 CHAIN)
    Chains: B
    Fragment: BROMELAIN RELEASED FRAGMENT
    Organism Scientific: INFLUENZA A VIRUS (A/X-31(H3N2))
    Organism Taxid: 132504
    Other Details: A RECOMBINANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
    Strain: X31
 
Molecule 3 - ANTIBODY (LIGHT CHAIN)
    Cell: HYBRIDROMAS
    Chains: L
    Fragment: FAB FRAGMENT OF ANTIBODY BH151
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 4 - ANTIBODY (HEAVY CHAIN)
    Cell: HYBRIDROMAS
    Chains: H
    Fragment: FAB FRAGMENT OF ANTIBODY BH151
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (3x): ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 21)
No.NameCountTypeFull Name
1MAN3Ligand/IonALPHA-D-MANNOSE
2NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:80 , ASN A:81 , PHE A:120BINDING SITE FOR RESIDUE NAG A 440
2AC2SOFTWAREASN A:165 , THR A:167 , SER A:219 , NAG A:451BINDING SITE FOR RESIDUE NAG A 450
3AC3SOFTWAREPRO A:221 , TRP A:222 , NAG A:450 , MAN A:452BINDING SITE FOR RESIDUE NAG A 451
4AC4SOFTWARETRP A:222 , NAG A:451BINDING SITE FOR RESIDUE MAN A 452
5AC5SOFTWARESER A:45 , ASN A:285 , VAL A:297 , ASN A:298 , NAG A:461 , HOH A:463BINDING SITE FOR RESIDUE NAG A 460
6AC6SOFTWARENAG A:460BINDING SITE FOR RESIDUE NAG A 461
7AC7SOFTWAREGLU B:150 , ASN B:154BINDING SITE FOR RESIDUE NAG B 410

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7H:22 -H:92
8H:140 -H:195
9L:23 -L:88
10L:133 -L:193

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:54 -Pro A:55
2Tyr L:139 -Pro L:140
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EO8)

(-) Exons   (0, 0)

(no "Exon" information available for 1EO8)

(-) 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:319
 aligned with HEMA_I68A0 | P03437 from UniProtKB/Swiss-Prot  Length:566

    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_I68A0     25 STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQ  343
               SCOP domains d1eo8a_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------1eo8A01 A:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                   ------------------------------------------------------- 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...ee..ee......ee...........ee......eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1eo8 A    9 STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQ  327
                                    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:175
 aligned with HEMA_I68A0 | P03437 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:175
                                   355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     
          HEMA_I68A0    346 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEEMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKG  520
               SCOP domains d1eo8b_ B: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains 1eo8B00 B:1-175  [code=3.90.20.10, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeeehhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1eo8 B    1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEEMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKG  175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1eo8h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                        d1eo8h2 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1eo8H01 H:1-113 Immunoglobulins                                                                                       1eo8H02 H:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...hhhhhee...eeeee........eeeee..........eeeeeeeeeee.........hhhh...eeee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1eo8 H    1 QVQLQQSGAELMKPGPSVKISCKATGYSFSTYFIEWIRQRPGHGLEWIGEILPGSDNTNFNEKFKDRATFTADTPSNTAYMQLSSLTSEDSAVYYCARPTGRLWFSYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205       
                                                                              52A                            82A||               100A                                                                                                                
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C                                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d1eo8l1 L:1-106B Immunoglobulin light chain kappa variable domain, VL-kappa                              d1eo8l2 L:107-211 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1eo8L01 L:1-107 Immunoglobulins                                                                           1eo8L02 L:108-211 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...eeee.....eeeeee........eeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee.....ee...eeeee.......eeee...hhhhhhh..eeeeeeeeee....eeee...........eeeee.........eeeeeeeee...hhhhh..eeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1eo8 L    1 QIILTQSPAIMSASPGEKVTMTCSASSDISYMHWYQQKSDTSPKIWIYDTSKLASGVPARFSGSGSGTSYSLTISTMEAEDAATYYCHQRSSYPTFGGGTKLEIKRADAAPTVSIFPPSKIQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  211
                                    10        20        30|       41        51        61        71        81        91   ||  102   ||  111       121       131       141       151       161       171       181       191       201       211
                                                        30|                                                             95|     106A|                                                                                                         
                                                         32                                                              97      106B
   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  (6, 6)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EO8)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMA_I68A0 | P03437: 1fyt 1ha0 1hgd 1hge 1hgf 1hgg 1hgh 1hgi 1hgj 1htm 1j8h 1ken 1kg0 1pyw 1qfu 1qu1 2hmg 2vir 2vis 2vit 2viu 2ypg 3eym 3hmg 3s4s 3s5l 3vun 3ztj 4c56 4hmg 5hmg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EO8)