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(-) Description

Title :  CYRSTAL STRUCTURE OF THE NATIVE 1918 H1N1 NEURAMINIDASE FROM A CRYSTAL WITH LATTICE-TRANSLOCATION DEFECTS
 
Authors :  X. Zhu, X. Xu, I. A. Wilson
Date :  25 Apr 08  (Deposition) - 05 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B  (2x)
Biol. Unit 1:  A,B  (2x)
Keywords :  6-Bladed Beta-Propeller, Glycoprotein, Glycosidase, Hydrolase, Membrane, Metal-Binding, Signal-Anchor, Transmembrane, Virion, Lattice-Translocation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, X. Xu, I. A. Wilson
Structure Determination Of The 1918 H1N1 Neuraminidase From A Crystal With Lattice-Translocation Defects
Acta Crystallogr. , Sect. D V. 64 843 2008
PubMed-ID: 18645233  |  Reference-DOI: 10.1107/S0907444908016648
(for further references see the PDB file header)

(-) 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 Vector Type: BACULOVIRUS
    Fragment: ECTODOMAIN OF NEURAMINIDASE
    Gene: NA
    Organism Scientific: INFLUENZA A VIRUS
    Strain: A/BREVIG MISSION/1/1918

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 36)

Asymmetric Unit (6, 36)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2CA7Ligand/IonCALCIUM ION
3GOL14Ligand/IonGLYCEROL
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (5, 21)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL10Ligand/IonGLYCEROL
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PO41Ligand/IonPHOSPHATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:146 , THR A:148 , ILE A:437BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWAREASN B:146 , THR B:148BINDING SITE FOR RESIDUE NAG B 2001
03AC5SOFTWARELYS A:366 , GLU A:375 , ARG A:394 , ILE A:400BINDING SITE FOR RESIDUE MAN B 2004
04AC6SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , ASN A:347BINDING SITE FOR RESIDUE CA A 1
05AC7SOFTWAREASP A:379 , ASN A:381 , ASP A:387 , SER A:389BINDING SITE FOR RESIDUE CA A 2
06AC8SOFTWAREASP B:379 , ASN B:381 , ASP B:387 , SER B:389BINDING SITE FOR RESIDUE CA B 3
07AC9SOFTWAREASP B:293 , GLY B:297 , ASP B:324 , GLY B:345 , ASN B:347BINDING SITE FOR RESIDUE CA B 4
08BC2SOFTWAREGLN A:249 , ALA A:250 , LEU A:268 , ASN A:269 , ALA A:270 , PRO A:271 , ASP B:311BINDING SITE FOR RESIDUE ACT A 3000
09BC3SOFTWAREARG B:152 , TRP B:178 , SER B:179BINDING SITE FOR RESIDUE ACT B 3001
10BC4SOFTWARETHR A:225 , GLU A:227 , GLU A:277BINDING SITE FOR RESIDUE ACT A 3002
11BC5SOFTWAREARG A:152 , TRP A:178BINDING SITE FOR RESIDUE ACT A 3003
12BC6SOFTWARETHR B:225 , GLU B:227 , GLU B:277BINDING SITE FOR RESIDUE ACT B 3004
13BC7SOFTWAREARG A:224 , GLU A:276 , GLU A:277 , ARG A:292 , ASN A:294BINDING SITE FOR RESIDUE PO4 A 1000
14BC8SOFTWAREASN A:170 , SER A:171 , GLU B:165BINDING SITE FOR RESIDUE GOL A 3004
15BC9SOFTWAREPRO A:93 , ILE A:94 , TYR A:356 , TRP A:361BINDING SITE FOR RESIDUE GOL A 3005
16CC1SOFTWAREPRO B:93 , ILE B:94 , TYR B:356 , TRP B:361 , TRP B:378BINDING SITE FOR RESIDUE GOL B 1002
17CC2SOFTWARESER A:90 , LEU A:91 , ASP A:283 , ARG A:355 , ASP A:357BINDING SITE FOR RESIDUE GOL A 1003
18CC3SOFTWARESER B:246 , GLU B:276 , GLU B:277 , ARG B:292BINDING SITE FOR RESIDUE GOL B 1004
19CC4SOFTWAREGLU A:165 , ASN A:170 , TYR B:169A , ASN B:170 , SER B:171BINDING SITE FOR RESIDUE GOL A 1005
20CC5SOFTWAREASP B:283 , MET B:288 , ARG B:355BINDING SITE FOR RESIDUE GOL B 1006
21CC6SOFTWARESER B:90 , LEU B:91 , ASP B:283 , ARG B:355 , TYR B:356 , ASP B:357BINDING SITE FOR RESIDUE GOL B 1007
22CC7SOFTWAREARG B:118 , GLU B:119 , ASP B:151 , ARG B:156 , TRP B:178BINDING SITE FOR RESIDUE GOL B 1008
23CC8SOFTWAREGLY A:331 , THR A:332 , ASP A:387 , SER A:388BINDING SITE FOR RESIDUE GOL A 1009

(-) 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, 12)

Asymmetric Unit
No.ModelResidues
11, 2Asn A:325 -Pro A:326
21, 2Gln A:430 -Pro A:431
31, 2Leu A:464 -Pro A:465
41, 2Asn B:325 -Pro B:326
51, 2Gln B:430 -Pro B:431
61, 2Leu B:464 -Pro B:465

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CYE)

(-) 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 d3cyea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3cyeA00 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
                3cye 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 d3cyeb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3cyeB00 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
                3cye 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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  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 3CYE)

(-) 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

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

UniProtKB/Swiss-Prot
        NRAM_I18A0 | Q9IGQ6: 3b7e 3beq

(-) Related Entries Specified in the PDB File

3beq THE SAME CRYSTAL BUT THE STRUCTURE WAS DETERMINED WITH DIFFERENT METHOD.