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(-) Description

Title :  SATELLITE TOBACCO MOSAIC VIRUS REFINED TO 1.4 A RESOLUTION USING ICOSAHEDRAL CONSTRAINTS
 
Authors :  S. B. Larson, J. S. Day, A. Mcpherson
Date :  07 Feb 14  (Deposition) - 10 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Double-Helix Rna, Protein-Rna Complex, Swiss Jelly-Roll Beta Barrel, Virus-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Larson, J. S. Day, A. Mcpherson
Satellite Tobacco Mosaic Virus Refined To 1. 4 Angstrom Resolution.
Acta Crystallogr. , Sect. D V. 70 2316 2014
PubMed-ID: 25195746  |  Reference-DOI: 10.1107/S1399004714013789
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A
    Organism Common: STMV
    Organism Scientific: SATELLITE TOBACCO MOSAIC VIRUS
    Organism Taxid: 12881
    Other Details: GROWN IN NICOTIANA TOBACUM PLANTS
 
Molecule 2 - RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
    Chains: B
    Organism Common: STMV
    Organism Scientific: SATELLITE TOBACCO MOSAIC VIRUS
    Organism Taxid: 12881
    Other Details: ARBITRARY RNA ADENINE NUCLEOTIDE DECAMER
 
Molecule 3 - RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
    Chains: C
    Organism Common: STMV
    Organism Scientific: SATELLITE TOBACCO MOSAIC VIRUS
    Organism Taxid: 12881
    Other Details: ARBITRARY RNA URIDINE NUCLEOTIDE DECAMER
 
Molecule 4 - RNA (5'-R(P*UP*U)-3')
    Chains: D
    Organism Common: STMV
    Organism Scientific: SATELLITE TOBACCO MOSAIC VIRUS
    Organism Taxid: 12881
    Other Details: ARBITRARY RNA URIDINE NUCLEOTIDE DIMER

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 180)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO460Ligand/IonPHOSPHATE ION
3SO4120Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:115 , ASN A:117 , MG A:204BINDING SITE FOR RESIDUE PO4 A 201
2AC2SOFTWAREASN A:117 , HOH A:371 , HOH A:515BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREPHE A:93 , ARG A:95 , HOH A:321 , HOH A:366 , HOH A:450 , HOH A:517 , HOH A:523 , HOH A:528BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREPO4 A:201BINDING SITE FOR RESIDUE MG A 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OQ8)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4OQ8)

(-) 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:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................eeeeeeeeee......eeee.hhhhhhhhh.....eeeeeeeeeee..........eeeeee..........eeee........eeeee.hhhhh.......eeeeeee...eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oq8 A  16 NSNVVTMIRAGSYPKVNPTPTWVRAIPFEVSVQSGIAFKVPVGSLFSANFRTDSFTSVTVMSVRAWTQLTPPVNEYSFVRLKPLFKTGDSTEEFEGRASNINTRASVGYRIPTNLRQNTVAADNVCEVRSNCRQVALVISCCFN 159
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155    


Chain B from PDB  Type:RNA  Length:10
                                          
                 4oq8 B 161 AAAAAAAAAA 170
                                   170


Chain C from PDB  Type:RNA  Length:10
                                          
                 4oq8 C 181 UUUUUUUUUU 190
                                   190


Chain D from PDB  Type:DNA/RNA  Length:2
                                  
                 4oq8 D 195 UU 196
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4OQ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OQ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OQ8)

(-) Gene Ontology  (3, 3)

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  4oq8
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  COAT_STMV | P17574
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 Related Entries

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

UniProtKB/Swiss-Prot
        COAT_STMV | P17574: 1a34 4nia 4oq9

(-) Related Entries Specified in the PDB File

1a34 THE SAME STRUCTURE REFINED AGAINST ROOM TEMPERATURE DATA USING STRICT ICOSAHEDRAL SYMMETRY CONSTRAINTS
4nia THE SAME STRUCTURE REFINED AGAINST ROOM TEMPERATURE DATA USING NCS RESTRAINTS
4oq9 THE SAME STRUCTURE REFINED AGAINST 100 K TEMPERATURE DATA USING NCS RESTRAINTS