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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 :  2.90
Chains :  Asym. Unit :  H,L,N
Biol. Unit 1:  H,L,N  (4x)
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: 11484
    Strain: (A/WHALE/MAINE/1/84(H13N9))
 
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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3MAN3Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN12Ligand/IonALPHA-D-MANNOSE
4NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN N:199 , ASN N:200 , LEU N:453 , GLY N:454 , GLN N:455 , NAG N:470B , HOH N:502 , HOH N:539BINDING SITE FOR RESIDUE NAG N 469A
02AC2SOFTWAREGLN N:392 , GLY N:394 , PHE N:452 , NAG N:469A , BMA N:471C , HOH N:502BINDING SITE FOR RESIDUE NAG N 470B
03AC3SOFTWARELEU N:377 , THR N:391 , GLY N:394 , NAG N:470B , MAN N:472D , HOH N:536BINDING SITE FOR RESIDUE BMA N 471C
04AC4SOFTWAREARG N:364 , GLU N:375 , BMA N:471C , MAN N:473E , MAN N:474FBINDING SITE FOR RESIDUE MAN N 472D
05AC5SOFTWAREVAL N:321 , ASP N:330 , ARG N:364 , LYS N:389 , PRO N:390 , MAN N:472D , MAN N:474FBINDING SITE FOR RESIDUE MAN N 473E
06AC6SOFTWAREARG 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
07AC7SOFTWAREGLU N:83 , ASN N:86 , GLN N:233 , ASN N:234BINDING SITE FOR RESIDUE NAG N 475A
08AC8SOFTWAREASN N:146 , TRP N:437 , NAG N:477BBINDING SITE FOR RESIDUE NAG N 476A
09AC9SOFTWARETRP N:437 , NAG N:476ABINDING SITE FOR RESIDUE NAG N 477B
10BC1SOFTWAREASP N:293 , ASN N:294 , GLY N:297 , ASP N:324 , ASN N:344 , ASN N:347BINDING SITE FOR RESIDUE CA N 0

(-) 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 1NCD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NCD)

(-) 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 d1ncdh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1ncdh2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1ncdH01 H:1-113 Immunoglobulins                                                                                         1ncdH02 H:114-218 Immunoglobulins                                                           --------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee........eeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.........eeeeeeee..eeeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ncd H    1 QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLEWMGWINTNTGEPTYGEEFKGRFAFSLETSASTANLQINNLKNEDKATFFCARGEDNFGSLSDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG  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 d1ncdl1 L:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1ncdl2 L:109-214 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1ncdL01 L:1-108 Immunoglobulins                                                                             1ncdL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeee....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee........eeeeeee...........eeeeee......eeeee..........eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeee.........eeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ncd 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_I84A1 | P05803 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_I84A1     82 SREFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRDLISWPLSSPPTVYNSRVECIGWSSTSCHDGRARMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCQNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLTGTAKHIEECSCYGEQAGVTCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEMLKVPNALTDDRSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNWPDGAKIEYFL  470
               SCOP domains d1ncdn_ N: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1ncdN00 N:81-468  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -Neur-1ncdN01 N:82-466                                                                                                                                                                                                                                                                                                                                                                             -- Pfam domains
         Sec.struct. author ...............eeeeeee.hhhhhhhh...eeeeeeeeeee..eeeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee...eeeeee.......ee..........eeeeeeeee.....eeeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeeee....eeeeee...................................ee......eeee.......eeeeeee..hhhhh......eeeeeeeeeee...eeee............eeeeeeeee.........eeeeeeeeeee.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ncd N   81 IREFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRDLISWPLSSPPTVYNSRVECIGWSSTSCHDGRARMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCQNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLTGTAKHIEECSCYGEQAGVTCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEMLKVPNALTDDRSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNWPDGAKIEYFL  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_I84A1 | P05803)
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 1nca 1ncb 1ncc 1ncw 1nd0 1ndg 1ndm 1orq 1plg 1ru9 1rua 1ruk 1rul 1rum 1rup 1yee 3fo9 3j3p 4fab 4zxb
        NRAM_I84A1 | P05803: 1nma 1nmb 2b8h

(-) Related Entries Specified in the PDB File

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