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(-) Description

Title :  AN EPIDEMIOLOGICALLY SIGNIFICANT EPITOPE OF A 1998 INFLUENZA VIRUS NEURAMINIDASE FORMS A HIGHLY HYDRATED INTERFACE IN THE NA-ANTIBODY COMPLEX.
 
Authors :  L. Venkatramani, E. Bochkareva, J. T. Lee, U. Gulati, W. G. Laver, A. Boc G. M. Air
Date :  23 Jul 05  (Deposition) - 20 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A,H,L  (4x)
Keywords :  Influenza Virus Neuraminidase-Fab Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Venkatramani, E. Bochkareva, J. T. Lee, U. Gulati, W. G. Laver, A. Bochkarev, G. M. Air
An Epidemiologically Significant Epitope Of A 1998 Human Influenza Virus Neuraminidase Forms A Highly Hydrated Interface In The Na-Antibody Complex
J. Mol. Biol. V. 356 651 2006
PubMed-ID: 16384583  |  Reference-DOI: 10.1016/J.JMB.2005.11.061

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A
    EC Number: 3.2.1.18
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 228928
    Strain: A/MEMPHIS/31/98(H3N2)
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA 6H3.2A11 (MEM5)
 
Molecule 3 - FAB LIGHT CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA 6H3.2A11 (MEM5)

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AHL
Biological Unit 1 (4x): AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric Unit (6, 16)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3GLC2Ligand/IonALPHA-D-GLUCOSE
4MAN5Ligand/IonALPHA-D-MANNOSE
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 60)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3GLC8Ligand/IonALPHA-D-GLUCOSE
4MAN20Ligand/IonALPHA-D-MANNOSE
5NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO44Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:245 , SER A:247 , ASP H:96 , ASN H:100 , ASP H:101 , HOH H:715 , HOH H:765 , TYR L:49 , TYR L:55 , SER L:56BINDING SITE FOR RESIDUE GLC H 701
02AC2SOFTWAREILE A:233 , ASN A:234 , THR A:236 , VAL A:307 , LYS A:308 , NAG A:634 , HOH A:878BINDING SITE FOR RESIDUE GLC A 702
03AC3SOFTWAREGLU A:83 , ASN A:86 , SER A:88 , TYR A:284 , NAG A:634 , HOH A:1047BINDING SITE FOR RESIDUE NAG A 686
04AC4SOFTWAREARG A:143 , ASN A:146 , TRP A:437 , HOH A:1039BINDING SITE FOR RESIDUE NAG A 646
05AC5SOFTWAREASN A:200 , TYR A:453 , GLY A:454 , THR A:455 , NAG A:704B , HOH A:809 , HOH A:858 , HOH A:865 , HOH A:977 , ASN L:92 , ARG L:93 , TYR L:94BINDING SITE FOR RESIDUE NAG A 703A
06AC6SOFTWAREASN A:393 , ARG A:394 , NAG A:703A , BMA A:705C , HOH A:869 , HOH A:977 , HOH A:982 , MAN L:217H , HOH L:297BINDING SITE FOR RESIDUE NAG A 704B
07AC7SOFTWAREGLN A:391 , ILE A:392 , ASN A:393 , ARG A:394 , NAG A:704B , MAN A:706D , HOH A:869 , HOH A:935 , MAN L:215FBINDING SITE FOR RESIDUE BMA A 705C
08AC8SOFTWAREGLN A:391 , ARG A:394 , BMA A:705C , MAN A:707E , HOH A:810 , HOH A:847 , HOH A:859 , HOH A:929BINDING SITE FOR RESIDUE MAN A 706D
09AC9SOFTWAREMAN A:706D , HOH A:1048BINDING SITE FOR RESIDUE MAN A 707E
10BC1SOFTWAREBMA A:705C , MAN L:216G , MAN L:217HBINDING SITE FOR RESIDUE MAN L 215F
11BC2SOFTWAREMAN L:215FBINDING SITE FOR RESIDUE MAN L 216G
12BC3SOFTWARENAG A:704B , ARG L:93 , MAN L:215F , HOH L:297BINDING SITE FOR RESIDUE MAN L 217H
13BC4SOFTWAREASN A:234 , TYR A:284 , PRO A:285 , NAG A:686 , GLC A:702BINDING SITE FOR RESIDUE NAG A 634
14BC5SOFTWAREASN A:329 , SER A:332 , HOH A:823 , HOH A:1054BINDING SITE FOR RESIDUE NAG A 629
15BC6SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , HIS A:347 , HOH A:808BINDING SITE FOR RESIDUE CA A 601
16BC7SOFTWAREARG A:118 , ASP A:151 , ARG A:292 , ARG A:371 , TYR A:406 , HOH A:857 , HOH A:1018BINDING SITE FOR RESIDUE SO4 A 602

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:175 -A:193
4A:183 -A:230
5A:232 -A:237
6A:278 -A:291
7A:280 -A:289
8A:318 -A:337
9A:421 -A:447
10H:22 -H:92
11L:23 -L:88

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Tyr A:284 -Pro A:285
2Thr A:325 -Pro A:326
3Arg A:430 -Lys A:431
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151
6Tyr L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AEP)

(-) 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:388
 aligned with Q9DL16_9INFA | Q9DL16 from UniProtKB/TrEMBL  Length:461

    Alignment length:388
                                    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        
        Q9DL16_9INFA     74 AEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKILFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI  461
               SCOP domains -d2aepa1 A:83-469 Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2aepA00 A:82-469  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee.........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee......eeeee....................................eeee..eeeeee.......eeeeeeee...........eeeeeeeeeeeee...eeeeeee....eeeeeeeeeeee.........eeeeeeeeeee.............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2aep A   82 AEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKILFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI  469
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461        


Chain H from PDB  Type:PROTEIN  Length:143
 aligned with HVM63_MOUSE | P84751 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
         HVM63_MOUSE      1 EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTMEYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSS  187
               SCOP domains ------------------------------------------------------------------------------------------------------------------------d2a                             eph1 H:1        14-190              SCOP domains
               CATH domains 2aepH01 H:1-113 Immunoglobulins                                                                                         ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee...eeeee...eeeee.....-----------------------------........--------.......-------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2aep H    1 EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTMEYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTLTVSSAKT-----------------------------FPEPVTLT--------GVHTFPA-------TLSSS  190
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |103       113  |      -         -         -  |    155       171    |    -  |    
                                                                              52A||                            82A||               100A             116                           148    155      170   176     186    
                                                                               52B|                             82B|                                                                                                   
                                                                                52C                              82C                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:129
 aligned with KVM5_MOUSE | P84750 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:129
                                                                                                                                                  121        
                                    10        20        30        40        50        60        70        80        90       100       110       120|        
          KVM5_MOUSE      1 DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQKKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELKRADAAPTVSIFPPS--------    -
               SCOP domains d2aepl1 L:1-107 automated matches                                                                          ---------------------- SCOP domains
               CATH domains 2aepL01 L:1-141 Immunoglobulins                                                                                        ---------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeeee..ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                2aep L    1 DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQKKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELKRADAAPLNNFYPKDTDQDSKDS  171
                                    10        20        30        40        50        60        70        80        90       100       110  ||   142||       
                                                                                                                                          113|    143|       
                                                                                                                                           136     164
   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  (3, 3)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9DL16_9INFA | Q9DL16)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain H   (HVM63_MOUSE | P84751)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain L   (KVM5_MOUSE | P84750)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  2aep
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  HVM63_MOUSE | P84751
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  KVM5_MOUSE | P84750
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  Q9DL16_9INFA | Q9DL16
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  3.2.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM63_MOUSE | P84751: 1zan 2adf 2aeq 2g2r 2g5b 2mpa 3bkc 3bkj 3bkm 4hdi

(-) Related Entries Specified in the PDB File

2aeq