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(-) Description

Title :  NEURAMINIDASE OF A/BREVIG MISSION/1/1918 H1N1 STRAIN IN COMPLEX WITH ZANAMIVIR
 
Authors :  X. Xu, X. Zhu, I. A. Wilson
Date :  30 Oct 07  (Deposition) - 07 Oct 08  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  6-Bladed Beta-Propeller, Glycosidase, Hydrolase, Membrane, Transmembrane, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xu, X. Zhu, R. A. Dwek, J. Stevens, I. A. Wilson
Structural Characterization Of The 1918 Influenza Virus H1N Neuraminidase
J. Virol. V. 82 10493 2008
PubMed-ID: 18715929  |  Reference-DOI: 10.1128/JVI.00959-08

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PACGP67
    Expression System Strain: HIGH-FIVE BTI-TN-5B1-4
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: SEQUENCE DATABASE RESIDUES 83-467
    Gene: NEURAMINIDASE
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/BREVIG MISSION/1/1918

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GOL9Ligand/IonGLYCEROL
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZMR2Ligand/IonZANAMIVIR
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL18Ligand/IonGLYCEROL
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZMR4Ligand/IonZANAMIVIR

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:146BINDING SITE FOR RESIDUE NAG B 1001
02AC2SOFTWAREASN B:247BINDING SITE FOR RESIDUE FUC B 1003
03AC3SOFTWAREASN A:146BINDING SITE FOR RESIDUE NAG A 1004
04AC4SOFTWAREASP B:379 , ASN B:381 , ASP B:387 , SER B:389BINDING SITE FOR RESIDUE CA B 1
05AC5SOFTWAREASP A:379 , ASN A:381 , ASP A:387 , SER A:389BINDING SITE FOR RESIDUE CA A 1
06AC6SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , ASN A:347BINDING SITE FOR RESIDUE CA A 1005
07AC7SOFTWAREASP B:293 , GLY B:297 , ASP B:324 , GLY B:345 , ASN B:347BINDING SITE FOR RESIDUE CA B 1004
08AC9SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:156 , TRP A:178 , ARG A:224 , GLU A:227 , SER A:246 , GLU A:276 , GLU A:277 , ARG A:292 , ARG A:371 , TYR A:406BINDING SITE FOR RESIDUE ZMR A 1001
09BC1SOFTWAREARG B:118 , GLU B:119 , ASP B:151 , ARG B:152 , ARG B:156 , TRP B:178 , ARG B:224 , GLU B:227 , SER B:246 , GLU B:276 , GLU B:277 , ARG B:292 , ARG B:371 , TYR B:406BINDING SITE FOR RESIDUE ZMR B 1002
10BC2SOFTWAREPRO B:93 , ILE B:94 , TYR B:356 , TRP B:361BINDING SITE FOR RESIDUE GOL B 1000
11BC3SOFTWAREPRO A:93 , ILE A:94 , TYR A:356 , TRP A:361 , TRP A:378BINDING SITE FOR RESIDUE GOL A 1007
12BC4SOFTWARESER B:95 , GLY B:96 , SER B:451 , ASP B:452 , THR B:453BINDING SITE FOR RESIDUE GOL B 1005
13BC5SOFTWARESER A:95 , GLY A:96 , SER A:451 , ASP A:452 , THR A:453BINDING SITE FOR RESIDUE GOL A 1008
14BC6SOFTWAREPRO A:169 , TYR A:169A , ASN A:170 , SER A:171 , GLU B:165BINDING SITE FOR RESIDUE GOL B 1006
15BC7SOFTWARETHR A:332BINDING SITE FOR RESIDUE GOL A 1009
16BC8SOFTWAREARG A:107 , HIS B:144 , ASN B:146 , GLY B:147 , THR B:148 , LYS B:150 , SER B:153BINDING SITE FOR RESIDUE GOL B 1007
17BC9SOFTWAREGLU A:165 , TYR B:169A , ASN B:170 , SER B:171BINDING SITE FOR RESIDUE GOL A 1010
18CC1SOFTWAREILE B:215 , TRP B:218 , LYS B:253 , SER B:265BINDING SITE FOR RESIDUE GOL B 1008

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:183 -A:230
4A:232 -A:237
5A:278 -A:291
6A:280 -A:289
7A:318 -A:336
8A:421 -A:447
9B:92 -B:417
10B:124 -B:129
11B:183 -B:230
12B:232 -B:237
13B:278 -B:291
14B:280 -B:289
15B:318 -B:336
16B:421 -B:447

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asn A:325 -Pro A:326
2Gln A:430 -Pro A:431
3Leu A:464 -Pro A:465
4Asn B:325 -Pro B:326
5Gln B:430 -Pro B:431
6Leu B:464 -Pro B:465

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B7E)

(-) Exons   (0, 0)

(no "Exon" information available for 3B7E)

(-) 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:385
 aligned with NRAM_I18A0 | Q9IGQ6 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:385
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462     
          NRAM_I18A0     83 VILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFSI  467
               SCOP domains d3b7ea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3b7eA00 A:83-468  [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..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3b7e A   83 VILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFSI  468
                                    92       102       112       122       132       142       152       162       171       181       191       201       211       221       231       241       251       261       271       281       291       301    || 312       322       332||||   345       355       365       375       385      |396       406      412D       422       432||     443       453       463     
                                                                                                                169A                                                                                                                                      306|                      333|||                                                  392|               412A|||                  433|                                 
                                                                                                                                                                                                                                                           308                       335||                                                   394                412B||                   435                                 
                                                                                                                                                                                                                                                                                      336|                                                                       412C|                                                       
                                                                                                                                                                                                                                                                                       339                                                                        412D                                                       


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with NRAM_I18A0 | Q9IGQ6 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:385
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462     
          NRAM_I18A0     83 VILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFSI  467
               SCOP domains d3b7eb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3b7eB00 B:83-468  [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..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3b7e B   83 VILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFSI  468
                                    92       102       112       122       132       142       152       162       171       181       191       201       211       221       231       241       251       261       271       281       291       301    || 312       322       332||||   345       355       365       375       385      |396       406      412D       422       432||     443       453       463     
                                                                                                                169A                                                                                                                                      306|                      333|||                                                  392|               412A|||                  433|                                 
                                                                                                                                                                                                                                                           308                       335||                                                   394                412B||                   435                                 
                                                                                                                                                                                                                                                                                      336|                                                                       412C|                                                       
                                                                                                                                                                                                                                                                                       339                                                                        412D
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B7E)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NRAM_I18A0 | Q9IGQ6)
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.

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 Related Entries

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        NRAM_I18A0 | Q9IGQ6: 3beq 3cye

(-) Related Entries Specified in the PDB File

3beq