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(-) Description

Title :  PHYSALIS MOTTLE VIRUS: NATURAL EMPTY CAPSID
 
Authors :  S. R. Sagurthi, V. Rajaram, H. S. Savithri, M. R. N. Murthy
Date :  27 Oct 09  (Deposition) - 03 Nov 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Plant Rna Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Sagurthi, V. Rajaram, H. S. Savithri, M. R. N. Murthy
Crystal Structure Of The Physalis Mottle Virus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Expression System: NICOTIANA GLUTINOSA
    Expression System Taxid: 35889
    Organism Scientific: PHYSALIS MOTTLE VIRUS
    Organism Taxid: 72539
    Other Details: NATURAL PURIFICATION FROM INFECTED PLANTS
    Synonym: VIRION PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2WWS)

(-) Sites  (0, 0)

(no "Site" information available for 2WWS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp C:58 -Pro C:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WWS)

(-) 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:161
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:161
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
            COAT_PHMV    28 QSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee.......eee...hhhhhhhhh.eeeeeeeeeeeeeee.hhhhh..eeeeeeee......hhhhhhh....eeeee..............hhhhh..eee.........eeeee............eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wws A  28 QSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:185
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
            COAT_PHMV     4 SEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......................eeeeeeeeeeeee.......eee...hhhhhhhhh.eeeeeeeeeeeeeeehhhhhhh...eeeeeee.....hhhhhhhh...eee..........eeeee........eee........eeeeee............eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wws B   4 SEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:185
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
            COAT_PHMV     4 SEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Tymo_coat-2wwsC01 C:8-179                                                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) ----Tymo_coat-2wwsC02 C:8-179                                                                                                                                                   --------- Pfam domains (2)
           Pfam domains (3) ----Tymo_coat-2wwsC03 C:8-179                                                                                                                                                   --------- Pfam domains (3)
         Sec.struct. author ..eee......................eeeeeeeeeeee.....eeeee.................eeeeeeeeeeee.hhhhh..eeeee.........hhhhhhhh...eeeee........eeeee........eee..........eeeee.............................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wws C   4 SEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
   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  (0, 0)

(no "SCOP Domain" information available for 2WWS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WWS)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (COAT_PHMV | P36351)
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: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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    Asp C:58 - Pro C:59   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        COAT_PHMV | P36351: 1e57 1qjz 2xpj

(-) Related Entries Specified in the PDB File

1e57 PHYSALIS MOTTLE VIRUS: EMPTY CAPSID
1qjz THREE DIMENSIONAL STRUCTURE OF PHYSALIS MOTTLE VIRUS: IMPLICATIONS FOR THE VIRAL ASSEMBLY