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(-) Description

Title :  CRYOEM HELICAL RECONSTRUCTION OF TMV
 
Authors :  P. Ge, Z. H. Zhou
Date :  26 Apr 11  (Deposition) - 01 Jun 11  (Release) - 21 Nov 12  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.30
Chains :  Asym. Unit :  A,R
Biol. Unit 1:  A,R  (49x)
Keywords :  Rna, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Ge, Z. H. Zhou
Hydrogen-Bonding Networks And Rna Bases Revealed By Cryo Electron Microscopy Suggest A Triggering Mechanism For Calcium Switches.
Proc. Natl. Acad. Sci. Usa V. 108 9637 2011
PubMed-ID: 21586634  |  Reference-DOI: 10.1073/PNAS.1018104108

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A
    Organism Scientific: TOBACCO MOSAIC VIRUS
    Organism Taxid: 12243
    Strain: VULGARE
 
Molecule 2 - 5'-R(P*AP*UP*G)-3'
    Chains: R
    Organism Scientific: TOBACCO MOSAIC VIRUS
    Organism Taxid: 12243
    Other Details: VIRAL RNA
    Strain: VULGARE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AR
Biological Unit 1 (49x): AR

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3J06)

(-) Sites  (0, 0)

(no "Site" information available for 3J06)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3J06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CAPSD_TMV_001 *T29ICAPSD_TMV  ---  ---AT28I
2UniProtVAR_CAPSD_TMV_002 *P79SCAPSD_TMV  ---  ---AP78S
3UniProtVAR_CAPSD_TMV_003 *E96DCAPSD_TMV  ---  ---AE95D
4UniProtVAR_CAPSD_TMV_004 *T104MCAPSD_TMV  ---  ---AT103M
5UniProtVAR_CAPSD_TMV_005 *G138RCAPSD_TMV  ---  ---AG137R
6UniProtVAR_CAPSD_TMV_006 *S149YCAPSD_TMV  ---  ---AS148Y
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 294)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CAPSD_TMV_001 *T29ICAPSD_TMV  ---  ---AT28I
2UniProtVAR_CAPSD_TMV_002 *P79SCAPSD_TMV  ---  ---AP78S
3UniProtVAR_CAPSD_TMV_003 *E96DCAPSD_TMV  ---  ---AE95D
4UniProtVAR_CAPSD_TMV_004 *T104MCAPSD_TMV  ---  ---AT103M
5UniProtVAR_CAPSD_TMV_005 *G138RCAPSD_TMV  ---  ---AG137R
6UniProtVAR_CAPSD_TMV_006 *S149YCAPSD_TMV  ---  ---AS148Y
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J06)

(-) Exons   (0, 0)

(no "Exon" information available for 3J06)

(-) Sequences/Alignments

Asymmetric Unit
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  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:155
 aligned with CAPSD_TMV | P69687 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:155
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     
            CAPSD_TMV     4 SITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPA 158
               SCOP domains d3j06a_ A: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhh.............................hhhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------I-------------------------------------------------S----------------D-------M---------------------------------R----------Y--------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j06 A   3 SITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPA 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     


Chain R from PDB  Type:RNA  Length:3
                                   
                 3j06 R   4 AUG   6
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J06)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (CAPSD_TMV | P69687)
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:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    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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  3j06
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  CAPSD_TMV | P69687
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_TMV | P69687: 1ei7 2tmv 3kml 4gqh 4udv

(-) Related Entries Specified in the PDB File

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