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(-) Description

Title :  THE REFINED THREE-DIMENSIONAL STRUCTURE OF AN INSECT VIRUS AT 2.8 ANGSTROMS RESOLUTION
 
Authors :  J. -P. Wery, V. S. Reddy, M. V. Hosur, J. E. Johnson
Date :  06 Jun 94  (Deposition) - 31 Aug 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,N
Biol. Unit 1:  A,B,C,D,E,F,N  (60x)
Keywords :  Protein-Rna Complex, Double Helix, Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Wery, V. S. Reddy, M. V. Hosur, J. E. Johnson
The Refined Three-Dimensional Structure Of An Insect Virus At 2. 8 A Resolution.
J. Mol. Biol. V. 235 565 1994
PubMed-ID: 8289282  |  Reference-DOI: 10.1006/JMBI.1994.1014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
    Chains: A, B, C
    Organism Scientific: BLACK BEETLE VIRUS
    Organism Taxid: 12285
    Other Details: GROWN IN DROSOPHILA MELANOGASTER
 
Molecule 2 - PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
    Chains: D, E, F
    Organism Scientific: BLACK BEETLE VIRUS
    Organism Taxid: 12285
    Other Details: GROWN IN DROSOPHILA MELANOGASTER
 
Molecule 3 - RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
    Chains: N
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFN
Biological Unit 1 (60x): ABCDEFN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:221 , GLY A:273 , ASP B:161BINDING SITE FOR RESIDUE CA A 364
2AC2SOFTWAREASP B:221 , GLY B:273 , ASP C:161BINDING SITE FOR RESIDUE CA B 364
3AC3SOFTWAREASP C:221 , GLY C:273BINDING SITE FOR RESIDUE CA C 364
4AC4SOFTWAREASP A:249 , GLU A:251 , ASP B:249 , GLU B:251 , ASP C:249 , GLU C:251BINDING SITE FOR RESIDUE CA C 365
5AC5SOFTWAREGLU A:251 , GLU B:251 , GLU C:251BINDING SITE FOR RESIDUE CA A 365

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BBV)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:262 -Pro A:263
2Leu B:262 -Pro B:263
3Leu C:262 -Pro C:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BBV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BBV)

(-) Exons   (0, 0)

(no "Exon" information available for 2BBV)

(-) 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:308
 aligned with CAPSD_BBV | P04329 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:308
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355        
            CAPSD_BBV    56 LTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVTRKDVLNQSINFTANRDTFILIAPTPGVAYWVADVPAGTFPISTTTFNAVNFPGFNSMFGNAAASRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSNVQFPVATTPATSALVHTLVGLDGVLAVGPDNFSESFIKGVFSQSVCNEPDFEFSDILEGIQTLPPANVTVATSGQPFNLAAGAEAVSGIVGWGNMDTIVIRVSAPTGAVNSAILKTWACLEYRPNPNAMLYQFGHDSPPCDEVALQEYRTVARSLPVAVIAAQN 363
               SCOP domains d2bbva_ A: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2bbvA00 A:56-363  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..................eeeeeeeeeeeeee..eeeeeeeeeee..eeeeeeeee.......eeeeeeeee.hhhhh.................eeeeeeeeee........eeeeeee..eeeeeeeee....eeeeeeeeeehhhhh.......eeeee...eeeee................eee..............eee................eeeeeee......eeeeeeeeeee.........hhhhh.......hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbv A  56 LTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVTRKDVLNQSINFTANRDTFILIAPTPGVAYWVADVPAGTFPISTTTFNAVNFPGFNSMFGNAAASRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSNVQFPVATTPATSALVHTLVGLDGVLAVGPDNFSESFIKGVFSQSVCNEPDFEFSDILEGIQTLPPANVTVATSGQPFNLAAGAEAVSGIVGWGNMDTIVIRVSAPTGAVNSAILKTWACLEYRPNPNAMLYQFGHDSPPCDEVALQEYRTVARSLPVAVIAAQN 363
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355        


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with CAPSD_BBV | P04329 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:308
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355        
            CAPSD_BBV    56 LTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVTRKDVLNQSINFTANRDTFILIAPTPGVAYWVADVPAGTFPISTTTFNAVNFPGFNSMFGNAAASRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSNVQFPVATTPATSALVHTLVGLDGVLAVGPDNFSESFIKGVFSQSVCNEPDFEFSDILEGIQTLPPANVTVATSGQPFNLAAGAEAVSGIVGWGNMDTIVIRVSAPTGAVNSAILKTWACLEYRPNPNAMLYQFGHDSPPCDEVALQEYRTVARSLPVAVIAAQN 363
               SCOP domains d2bbvb_ B: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2bbvB00 B:56-363  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..................eeeeeeeeeeeeee..eeeeeeeeeee..eeeeeeeee.......eeeeeeeee.hhhhh.................eeeeeeeeee........eeeeeee..eeeeeeeee....eeeeeeeeeehhhhh.......eeeee...eeeee................eee..............eee................eeeeeee......eeeeeeeeeee.........hhhhh.......hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbv B  56 LTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVTRKDVLNQSINFTANRDTFILIAPTPGVAYWVADVPAGTFPISTTTFNAVNFPGFNSMFGNAAASRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSNVQFPVATTPATSALVHTLVGLDGVLAVGPDNFSESFIKGVFSQSVCNEPDFEFSDILEGIQTLPPANVTVATSGQPFNLAAGAEAVSGIVGWGNMDTIVIRVSAPTGAVNSAILKTWACLEYRPNPNAMLYQFGHDSPPCDEVALQEYRTVARSLPVAVIAAQN 363
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355        


Chain C from PDB  Type:PROTEIN  Length:321
 aligned with CAPSD_BBV | P04329 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:344
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359    
            CAPSD_BBV    20 TQTAPVPQQNVPKQPRRRRNRARRNRRQGRAMNMGALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVTRKDVLNQSINFTANRDTFILIAPTPGVAYWVADVPAGTFPISTTTFNAVNFPGFNSMFGNAAASRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSNVQFPVATTPATSALVHTLVGLDGVLAVGPDNFSESFIKGVFSQSVCNEPDFEFSDILEGIQTLPPANVTVATSGQPFNLAAGAEAVSGIVGWGNMDTIVIRVSAPTGAVNSAILKTWACLEYRPNPNAMLYQFGHDSPPCDEVALQEYRTVARSLPVAVIAAQN 363
               SCOP domains d2bbvc_ C: A                       lphanodavirus capsid protein                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2bbvC00 C:20                       -363  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............-----------------------......hhhhhhhhhhhhh..................eeeeeeeeeeeeee..eeeeeeeeeee..eeeeeeeee.......eeeeeeeee.hhhhh.................eeeeeeeeee........eeeeeee..eeeeeeeee....eeeeeeeeeehhhhh.......eeeee...eeeee................eee..............eee................eeeeeee......eeeeeeeeeee.........hhhhh.......hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbv C  20 TQTAPVPQQNVP-----------------------ALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVTRKDVLNQSINFTANRDTFILIAPTPGVAYWVADVPAGTFPISTTTFNAVNFPGFNSMFGNAAASRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSNVQFPVATTPATSALVHTLVGLDGVLAVGPDNFSESFIKGVFSQSVCNEPDFEFSDILEGIQTLPPANVTVATSGQPFNLAAGAEAVSGIVGWGNMDTIVIRVSAPTGAVNSAILKTWACLEYRPNPNAMLYQFGHDSPPCDEVALQEYRTVARSLPVAVIAAQN 363
                                    29 |       -         -     |  59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359    
                                      31                      55                                                                                                                                                                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:16
 aligned with CAPSD_BBV | P04329 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:16
                                   373      
            CAPSD_BBV   364 ASMWERVKSIIKSSLA 379
               SCOP domains ---------------- SCOP domains
               CATH domains 2bbvD00          CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2bbv D 364 ASMWERVKSIIKSSLA 379
                                   373      


Chain E from PDB  Type:PROTEIN  Length:16
 aligned with CAPSD_BBV | P04329 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:16
                                   373      
            CAPSD_BBV   364 ASMWERVKSIIKSSLA 379
               SCOP domains ---------------- SCOP domains
               CATH domains 2bbvE00          CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2bbv E 364 ASMWERVKSIIKSSLA 379
                                   373      


Chain F from PDB  Type:PROTEIN  Length:16
 aligned with CAPSD_BBV | P04329 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:16
                                   373      
            CAPSD_BBV   364 ASMWERVKSIIKSSLA 379
               SCOP domains ---------------- SCOP domains
               CATH domains 2bbvF00          CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2bbv F 364 ASMWERVKSIIKSSLA 379
                                   373      


Chain N from PDB  Type:RNA  Length:10
                                          
                 2bbv N   1 UCUUAUAUCU  10
                                    10
   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 2BBV)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (CAPSD_BBV | P04329)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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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  2bbv
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 Related Entries

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