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(-) Description

Title :  CRYSTAL STRUCTURE OF PHYSALIS MOTTLE VIRUS WITH INTACT ORDERED RNA
 
Authors :  S. R. Sagurthi, V. Rajaram, H. S. Savithri, M. R. N. Murthy
Date :  26 Aug 10  (Deposition) - 15 Sep 10  (Release) - 08 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Virus, Plant Rna Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Sagurthi, V. Rajaram, H. S. Savithri, M. R. N. Murthy
Crystal Structure Of Natural Bottom Component Of Phmv
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Organism Scientific: PHYSALIS MOTTLE VIRUS
    Organism Taxid: 72539
    Other Details: PLANT VIRUS
 
Molecule 2 - 5'-R(CP*CP*CP)-3'
    Chains: D
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2XPJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XPJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XPJ)

(-) 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:165
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:165
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
            COAT_PHMV    24 PNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xpjA00 A:24-188  [code=2.60.120.20, no name defined]                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeee...hhhhhhhhh.eeeeeeeeeeeeeee.hhhhhh...eeeeeee.....hhhhhhh....eee...........eeee...................eeeeee............eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpj A  24 PNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     


Chain B from PDB  Type:PROTEIN  Length:180
 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 2xpjB00 B:4-188  [co     de=2.60.120.20, no name defined]                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.......ee......-----...eeeeeeeeeeee....eeeeee...hhhhhhhhh....eeeeeeeeeeeehhhhhhh.eeeeeeeee.....hhhhhhhh...eeeee........eeeee....ee..eee........eeeeeee...........eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpj B   4 SEVVKVKQASIPAPGSILSQ-----SPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    13        23     |  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
                                              23    29                                                                                                                                                               


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 2xpjC00 C:4-188  [code=2.60.120.20, no name defined]                                                                                                                                      CATH domains
           Pfam domains (1) ----Tymo_coat-2xpjC01 C:8-179                                                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) ----Tymo_coat-2xpjC02 C:8-179                                                                                                                                                   --------- Pfam domains (2)
           Pfam domains (3) ----Tymo_coat-2xpjC03 C:8-179                                                                                                                                                   --------- Pfam domains (3)
         Sec.struct. author ..eee......................eeeeeeeeeeeee.....eeeee...hhhhhhhhh.eeeeeeeeeeeeeeehhhhhhh.eeeeeeee......hhhhhhhh...eeeee........eeeee........eee.........eeeee............eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpj C   4 SEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     


Chain D from PDB  Type:RNA  Length:3
                                   
                 2xpj D   1 CCC   3
   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 2XPJ)

(-) CATH Domains  (1, 3)

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

(-) 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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 Related Entries

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

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

(-) 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
2wws PHYSALIS MOTTLE VIRUS: NATURAL EMPTY CAPSID