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(-) Description

Title :  THE 2.3 A STRUCTURE OF PORCINE CIRCOVIRUS 2
 
Authors :  R. Khayat, J. A. Speir, J. E. Johnson
Date :  08 Mar 11  (Deposition) - 15 Jun 11  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Biol. Unit 2:  A  (60x)
Keywords :  Viral Jelly Roll, Beta Barrel, Ssdna, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Khayat, N. Brunn, J. A. Speir, J. M. Hardham, R. G. Ankenbauer, A. Schneemann, J. E. Johnson
The 2. 3-Angstrom Structure Of Porcine Circovirus 2.
J. Virol. V. 85 7856 2011
PubMed-ID: 21632760  |  Reference-DOI: 10.1128/JVI.00737-11

(-) Compounds

Molecule 1 - PORCINE CIRCOVIRUS 2 (PCV2) CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 42-231
    Gene: CAP, CAP, ORF2, CP
    Organism Common: PCV2
    Organism Scientific: PORCINE CIRCOVIRUS 2
    Organism Taxid: 85708
    Synonym: CAP PROTEIN, CAPSID PROTEIN, ORF2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (60x): A
Biological Unit 2 (60x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 240)
No.NameCountTypeFull Name
1SO4240Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:84 , ARG A:181 , GLN A:183 , THR A:184 , ALA A:185 , HOH A:254BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWARELYS A:95 , TYR A:155 , PHE A:156 , THR A:157 , ASN A:172 , HOH A:296 , HOH A:304 , HOH A:336BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREPRO A:105 , HOH A:267BINDING SITE FOR RESIDUE SO4 A 302
4AC4SOFTWAREASN A:173 , ARG A:175 , ASN A:176BINDING SITE FOR RESIDUE SO4 A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R0R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:147 -Pro A:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R0R)

(-) Exons   (0, 0)

(no "Exon" information available for 3R0R)

(-) 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:194
 aligned with Q805N7_PCV2 | Q805N7 from UniProtKB/TrEMBL  Length:233

    Alignment length:201
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
          Q805N7_PCV2    31 HPRHRYRWRRKNGIFNTRLSRTFGYTIKRTTVKTPSWAVDMMRFNINDFLPPGGGSNPRSVPFEYYRIRKVKVEFWPCSPITQGDRGVGSSAVILDDNFVTKATALTYDPYVNYSSRHTITQPFSYHSRYFTPKPVLDSTIDYFQPNNKRNQLWLRLQTAGNVDHVGLGTAFENSIYDQEYNIRVTMYVQFREFNLKDPPL 231
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Circo_capsid-3r0rA01 A:37-221                                                                                                                                                            ----- Pfam domains
         Sec.struct. author hh-------hhh.eeeeeeeeeeeeee.........eeeeeeeehhhhh..eee..eee...eeeeeeeeeeeeeee..........eeeeee.........eeee...........eeee.....eeeee..ee............hhhhh..ee........eeeeeeeee.....eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0r A  33 HP-------FTNGIFNTRLSRTFGYTIKRTTVKTPSWAVDMMRFNINDFLPPGGGSNPRSVPFEYYRIRKVKVEFWPCSPITQGDRGVGSSAVILDDNFVTKATALTYDPYVNYSSRHTITQPFSYHSRYFTPKPVLDSTIDYFQPNNKRNQLWLRLQTAGNVDHVGLGTAFENSIYDQEYNIRVTMYVQFREFNLKDPPL 226
                             |      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225 
                             |      35                                                                                                                                                                                               
                            34
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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  (0, 0)

(no "SCOP Domain" information available for 3R0R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R0R)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q805N7_PCV2 | Q805N7)
biological process
    GO:0019069    viral capsid assembly    The assembly of a virus capsid from its protein subunits.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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