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(-) Description

Title :  NODAMURA VIRUS
 
Authors :  P. Natarajan, J. E. Johnson
Date :  16 Sep 97  (Deposition) - 14 Jan 98  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (60x)
Keywords :  Insect Virus, Nodamura Virus, Coat Protein, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Zlotnick, P. Natarajan, S. Munshi, J. E. Johnson
Resolution Of Space-Group Ambiguity And Structure Determination Of Nodamura Virus To 3. 3 A Resolution From Pseudo-R32 (Monoclinic) Crystals.
Acta Crystallogr. , Sect. D V. 53 738 1997
PubMed-ID: 15299863  |  Reference-DOI: 10.1107/S0907444997007427
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NODAMURA VIRUS COAT PROTEINS
    Chains: A, B, C
    Engineered: YES
    Expression System: GALLERIA MELLONELLA
    Expression System Common: GREATER WAX MOTH
    Expression System Taxid: 7137
    Organism Scientific: NODAMURA VIRUS
    Organism Taxid: 12288
    Other Details: THE COAT PROTEIN PRECURSOR IS ENZYMATICALLY CLEAVED INTO COAT PROTEINS BETA AND GAMMA. CHAINS A, B, AND C ARE THE BETA PROTEIN, CHAINS D, E, AND F ARE THE GAMMA PROTEIN
    Other Details - Source: GROWN IN WAX MOTH LARVAE
 
Molecule 2 - NODAMURA VIRUS COAT PROTEINS
    Chains: D, E, F
    Organism Scientific: NODAMURA VIRUS
    Organism Taxid: 12288
    Other Details: THE COAT PROTEIN PRECURSOR IS ENZYMATICALLY CLEAVED INTO COAT PROTEINS BETA AND GAMMA. CHAINS A, B, AND C ARE THE BETA PROTEIN, CHAINS D, E, AND F ARE THE GAMMA PROTEIN
    Other Details - Source: GROWN IN WAX MOTH LARVAE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (60x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NOV)

(-) Sites  (0, 0)

(no "Site" information available for 1NOV)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1C:69 -C:318

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NOV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NOV)

(-) 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:309
 aligned with CAPSD_NODAM | P12871 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:309
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
          CAPSD_NODAM    47 NMLKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN 355
               SCOP domains d1nova_ A: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1novA00 A:55-363  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.hhh.................eeeeeeeeeeeee...eeeeeee.....eeeeeeeee..........eeee...hhhh...........eeeeee...eeeeee.........eeeeeee...eeeeeeeeee.....eeeeeeeeee..hhhhh......eeee.....eee..................................................eeeeeeee.....eeeeeeeeeeeeeee.................hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nov A  55 NMLKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN 363
                                    64        74        84        94       104       114       124       135       145       155       165       175       185       195       205|||| ||211       221       231       241       251       261       271       281|      294       304       314       324       334       344       354         
                                                                                                        133|                                                                    206||| ||                                                                      281|                                                                              
                                                                                                         135                                                                     501|| ||                                                                       285                                                                              
                                                                                                                                                                                  207| ||                                                                                                                                                        
                                                                                                                                                                                   502 ||                                                                                                                                                        
                                                                                                                                                                                     504|                                                                                                                                                        
                                                                                                                                                                                      208                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with CAPSD_NODAM | P12871 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:309
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
          CAPSD_NODAM    47 NMLKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN 355
               SCOP domains d1novb_ B: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1novB00 B:55-363  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh......................eeeeeeeeeeeee...eeeeeee.....eeeeeeeee..........eeee....hhhh......hhh.eeeeee..eeeeeee.........eeeeeee..eeeeeeeeeee.....eeeeeeeeeee.hhhhh......eeee.....eeee.................................................eeeeeeee.....eeeeeeeeeeeeeee....hhhhh........hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nov B  55 NMLKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN 363
                                    64        74        84        94       104       114       124       135       145       155       165       175       185       195       205|||| ||211       221       231       241       251       261       271       281|      294       304       314       324       334       344       354         
                                                                                                        133|                                                                    206||| ||                                                                      281|                                                                              
                                                                                                         135                                                                     501|| ||                                                                       285                                                                              
                                                                                                                                                                                  207| ||                                                                                                                                                        
                                                                                                                                                                                   502 ||                                                                                                                                                        
                                                                                                                                                                                     504|                                                                                                                                                        
                                                                                                                                                                                      208                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:324
 aligned with CAPSD_NODAM | P12871 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:348
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347        
          CAPSD_NODAM     8 RRRAAPRQQQRQQSNRASNQPRRRRARRTRRQQRMAATNNMLKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN 355
               SCOP domains d1novc_ C: Alphan                        odavirus capsid protein                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1novC00 C:13-363                          [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.........------------------------....hhhhhhhhhhhhhhh.................eeeeeeeeeeeee...eeeeeee.....eeeeeeeee..........eeee...hhhh....hhhhhh.eeeeee..eeeeeee.........eeeeeee...eeeeeeeeee.....eeeeeeeeee..hhhhh......eeee.....eeee.................................................eeeeeeee.....eeeeeeeeeeeeeee.....hhhh........hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nov C  13 RRRAAPRQQQRQQSNRA------------------------LKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN 363
                                    22      |  -         -         - |      65        75        85        95       105       115       125       136       146       156       166       176       186       196       206||| || 212       222       232       242       252       262       272       285       295       305       315       325       335       345       355        
                                           29                       57                                                                         133|                                                                    206||| ||                                                                      281|                                                                              
                                                                                                                                                135                                                                     501|| ||                                                                       285                                                                              
                                                                                                                                                                                                                         207| ||                                                                                                                                                        
                                                                                                                                                                                                                          502 ||                                                                                                                                                        
                                                                                                                                                                                                                            504|                                                                                                                                                        
                                                                                                                                                                                                                             208                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:20
 aligned with CAPSD_NODAM | P12871 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:20
                                   365       375
          CAPSD_NODAM   356 ATFWERVRSILKSGLNFAST 375
               SCOP domains -------------------- SCOP domains
               CATH domains 1novD00 D:364-383    CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 1nov D 364 ATFWERVRSILKSGLNFAST 383
                                   373       383


Chain E from PDB  Type:PROTEIN  Length:17
 aligned with CAPSD_NODAM | P12871 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:17
                                   365       
          CAPSD_NODAM   356 ATFWERVRSILKSGLNF 372
               SCOP domains ----------------- SCOP domains
               CATH domains 1novE00 E:364-380 CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 1nov E 364 ATFWERVRSILKSGLNF 380
                                   373       


Chain F from PDB  Type:PROTEIN  Length:17
 aligned with CAPSD_NODAM | P12871 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:17
                                   365       
          CAPSD_NODAM   356 ATFWERVRSILKSGLNF 372
               SCOP domains ----------------- SCOP domains
               CATH domains 1novF00 F:364-380 CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 1nov F 364 ATFWERVRSILKSGLNF 380
                                   373
   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  (1, 3)

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

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NOV)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (CAPSD_NODAM | P12871)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0039665    permeabilization of host organelle membrane involved in viral entry into host cell    Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    GO:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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