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(-) Description

Title :  THE STRUCTURE OF B19 PARVOVIRUS CAPSID
 
Authors :  B. Kaufmann, A. A. Simpson, M. G. Rossmann
Date :  20 Jan 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Icosahedral Capsid, Beta-Barrel, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Kaufmann, A. A. Simpson, M. G. Rossmann
The Structure Of Human Parvovirus B19.
Proc. Natl. Acad. Sci. Usa V. 101 11628 2004
PubMed-ID: 15289612  |  Reference-DOI: 10.1073/PNAS.0402992101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - B19 PARVOVIRUS CAPSID
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: ACMNPV-VP2
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: VP2 CAPSID PROTEIN
    Gene: VP2
    Organism Scientific: HUMAN PARVOVIRUS B19
    Organism Taxid: 10798

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S58)

(-) Sites  (0, 0)

(no "Site" information available for 1S58)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S58)

(-) Exons   (0, 0)

(no "Exon" information available for 1S58)

(-) 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:523
 aligned with Q90201_PAVHB | Q90201 from UniProtKB/TrEMBL  Length:554

    Alignment length:536
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548      
         Q90201_PAVHB    19 NPVKSMWSEGATFSANSVTCTFSRQFLIPYDPEHHYKVFSPAASSCHNASGKEAKVCTISPIMGYSTPWRYLDFNALNLFFSPLEFQHLIENYGSIAPDALTVTISEIAVKDVTDKTGGGVQVTDSTTGRLCMLVDHEYKYPYVLGQGQDTLAPELPIWVYFPPQYAYLTVGDVNTQGISGDSKKLASEESAFYVLEHSSFQLLGTGGTATMSYKFPPVPPENLEGCSQHFYEMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTKEGDSSNTGAGKALTGLSTGTSQNTRISLRPGPVSQPYHHWDTDKYVTGINAISHGQTTYGNAEDKEYQQGVGRFPNEKEQLKQLQGLNMHTYFPNKGTQQYTDQIERPLMVGSVWNRRALHYESQLWSKIPNLDDSFKTQFAALGGWGLHQPPPQIFLKILPQSGPIGGIKSMGITTLVQYAVGIMTVTMTFKLGPRKATGRWNPQPGVYPPHAAGHLPYVLYDPTATDAKQHHRHGYEKPEELWTAKSRVHPL 554
               SCOP domains d1s58a_ A: Parvovirus (panleukopenia virus) capsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1s58A00 A:19-554 Empty Capsid Viral Protein 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains Parvo_coat-1s58A01 A:19-521                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eeeeeeeeeeee....................................ee.........hhhhhh.hhhhhhhhhhh....eeeeeeee.....eeee.......ee..........ee...............................ee....eee........eee.......................eeeeee..........ee..hhhhh................................................-------------.........................ee....ee..............................hhhhh..........................................................................ee......ee..........ee..eeeeeeeeeeeee..........................................................ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s58 A  19 NPVKSMWSEGATFSANSVTCTFSRQFLIPYDPEHHYKVFSPAASSCHNASGKEAKVCTITPIMGYSTPWRYLDFNALNLFFSPLEFQHLIENYGSIAPDALTVTISEIAVKDVTDKTGGGVQVTDSATGRLCMLVDHEYKYPYVLGQGQDTLAPELPIWVYFPPQYAYLTVGDVNTQGISGDSKKLASEESAFYVLEHSSFQLLGTGGTATMSYKFPPVPPENLEGCSQHFYEMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTK-------------TGLSTGTSQNTRISLRPGPVSQPYHHWDTDKYVTGINAISHGQTTYGNAEDKEYQQGVGRFPNEKEQLKQLQGLNMHTYFPNKGTQQYTDQIERPLMVGSVWNRRALHYESQLWSKIPNLDDSFKTQFAALGGWGLHQPPPQIFLKILPQSGPIGGIKSMGITTLVQYAVGIMTVTMTFKLGPRKATGRWNPQPGVYPPHAAGHLPYVLYDPTATDAKQHHRHGYEKPEELWTAKSRVHPL 554
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 |       -     | 318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548      
                                                                                                                                                                                                                                                                                                                   300           314
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Parvo_coat] (8)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q90201_PAVHB | Q90201)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    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.

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  1s58
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1S58)

(-) Related Entries Specified in the PDB File

1dnv GALLERIA MELLONELLA DENSOVIRUS
1fpv FELINE PANLEUKOPENIA VIRUS
1k3v PORCINE PARVOVIRUS
1lp3 ADENO-ASSOCIATED VIRUS
1mvm MINUTE VIRUS OF MICE
4dpv CANINE PARVOVIRUS