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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX
 
Authors :  W. R. Tulip, J. N. Varghese, P. M. Colman
Date :  21 Jan 92  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  H,L,N
Biol. Unit 1:  H,L,N  (4x)
Biol. Unit 2:  H (8x),L (4x),N (8x)
Keywords :  Hydrolase(O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. R. Tulip, J. N. Varghese, W. G. Laver, R. G. Webster, P. M. Colman
Refined Crystal Structure Of The Influenza Virus N9 Neuraminidase-Nc41 Fab Complex.
J. Mol. Biol. V. 227 122 1992
PubMed-ID: 1381757  |  Reference-DOI: 10.1016/0022-2836(92)90687-F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INFLUENZA A SUBTYPE N9 NEURAMINIDASE
    Chains: N
    EC Number: 3.2.1.18
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 384509
    Strain: (A/TERN/AUSTRALIA/G70C/1975(H11N9))
 
Molecule 2 - IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLN
Biological Unit 1 (4x): HLN
Biological Unit 2 (8x): H (8x)L (4x)N (8x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3MAN3Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 32)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN12Ligand/IonALPHA-D-MANNOSE
4NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 64)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN24Ligand/IonALPHA-D-MANNOSE
4NAG32Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH N:72 , ASN N:199 , ASN N:200 , LEU N:453 , GLY N:454 , GLN N:455 , NAG N:470BBINDING SITE FOR RESIDUE NAG N 469A
2AC2SOFTWAREHOH N:32 , GLN N:392 , GLY N:394 , PHE N:452 , NAG N:469A , BMA N:471CBINDING SITE FOR RESIDUE NAG N 470B
3AC3SOFTWAREHOH N:69 , LEU N:377 , THR N:391 , GLY N:394 , NAG N:470B , MAN N:472DBINDING SITE FOR RESIDUE BMA N 471C
4AC4SOFTWAREARG N:364 , GLU N:375 , BMA N:471C , MAN N:473E , MAN N:474FBINDING SITE FOR RESIDUE MAN N 472D
5AC5SOFTWAREASP N:330 , LYS N:389 , PRO N:390 , MAN N:472D , MAN N:474FBINDING SITE FOR RESIDUE MAN N 473E
6AC6SOFTWAREARG N:327 , ASN N:329 , ASP N:330 , ARG N:364 , ILE N:366 , ILE N:368 , MAN N:472D , MAN N:473EBINDING SITE FOR RESIDUE MAN N 474F
7AC7SOFTWAREASN N:86 , HIS N:233 , ASN N:234BINDING SITE FOR RESIDUE NAG N 475A
8AC8SOFTWAREASN N:146BINDING SITE FOR RESIDUE NAG N 476A
9AC9SOFTWAREASP N:293 , GLY N:297 , ASP N:324 , ASN N:347BINDING SITE FOR RESIDUE CA N 1

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194
5L:214 -H:128
6N:92 -N:417
7N:124 -N:129
8N:175 -N:193
9N:183 -N:230
10N:232 -N:237
11N:278 -N:291
12N:280 -N:289
13N:318 -N:337
14N:421 -N:447

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asn N:325 -Pro N:326
2Arg N:430 -Pro N:431
3Ser L:7 -Pro L:8
4Pro L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Phe H:148 -Pro H:149
7Glu H:150 -Pro H:151
8Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NCA)

(-) 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 H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d1ncah1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1ncah2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1ncaH01 H:1-114 Immunoglobulins                                                                                          1ncaH02 H:115-227 Immunoglobulins                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee........eeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nca H    1 QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTNTGEPTYGEEFKGRFAFSLETSASTANLQINNLKNEDTATFFCARGEDNFGSLSDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123      |135       145       156||     171       183       193  || ||205||     216       226 
                                                                              52A                            82A||               100A||                           130|                  154|||    169|      180|          196| || 206|                   
                                                                                                              82B|                100B|                            133                   156||     171       183           198 ||  208                   
                                                                                                               82C                 100C                                                   157|                               200|                        
                                                                                                                                                                                           162                                202                        


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1ncal1 L:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1ncal2 L:109-214 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1ncaL01 L:1-108 Immunoglobulins                                                                             1ncaL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee........eeeeeee...........eeeee.......eeeee..........eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeee.........eeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nca L    1 DIVMTQSPKFMSTSVGDRVTITCKASQDVSTAVVWYQQKPGQSPKLLIYWASTRHIGVPDRFAGSGSGTDYTLTISSVQAEDLALYYCQQHYSPPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain N from PDB  Type:PROTEIN  Length:389
 aligned with NRAM_I75A5 | P03472 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:389
                                    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         
          NRAM_I75A5     82 IRDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL  470
               SCOP domains d1ncan_ N: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1ncaN00 N:81-468  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains Neur-1ncaN01 N:81-466                                                                                                                                                                                                                                                                                                                                                                              -- Pfam domains
         Sec.struct. author ...............eeeeeee.hhhhhhhh...eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee.......ee..........eeeeeeeee.....eeeeeeeee..eeeeeee...........eeeee..eeeee..........eeeeee....eeeeee...................................ee......eeee.......eeeeeee..hhhhh......eeeeeeeeeee...eeeee..........eeeeeeeeee.........eeeeeeeeeee.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nca N   81 IRDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL  468
                                    90       100       110       120       130       140       150       160      169A       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329   ||  340       350       360       370       380       390 ||    401       411 ||    419       429       439       449       459         
                                                                                                                  169A                                                                                                                                                                 333|                                                      392|               412A|                                                        
                                                                                                                                                                                                                                                                                        335                                                       394                412B
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 5)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Sialidase (56)

(-) Gene Ontology  (42, 44)

Asymmetric Unit(hide GO term definitions)
Chain N   (NRAM_I75A5 | P03472)
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
        GCAM_MOUSE | P01865: 1axt 1dqj 1e4w 1egj 1flr 1fpt 1ggb 1ggc 1kb5 1lo0 1nby 1nbz 1ncb 1ncc 1ncd 1ncw 1nd0 1ndg 1ndm 1orq 1plg 1ru9 1rua 1ruk 1rul 1rum 1rup 1yee 3fo9 3j3p 4fab 4zxb
        NRAM_I75A5 | P03472: 1a14 1bji 1f8b 1f8c 1f8d 1f8e 1iny 1l7f 1l7g 1l7h 1mwe 1ncb 1ncc 1nmc 1nna 1nnb 1nnc 1xoe 1xog 2c4a 2c4l 2qwa 2qwb 2qwc 2qwd 2qwe 2qwf 2qwg 2qwh 2qwi 2qwj 2qwk 3nn9 3w09 4dgr 4nn9 4weg 5nn9 6nn9 7nn9

(-) Related Entries Specified in the PDB File

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