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A model for the structure of satellite tobacco mosaic virus. 2012

Yingying Zeng, and Steven B Larson, and Christine E Heitsch, and Alexander McPherson, and Stephen C Harvey
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Satellite tobacco mosaic virus (STMV) is an icosahedral T=1 single-stranded RNA virus with a genome containing 1058 nucleotides. X-ray crystallography revealed a structure containing 30 double-helical RNA segments, with each helix having nine base pairs and an unpaired nucleotide at the 3' end of each strand. Based on this structure, Larson and McPherson proposed a model of 30 hairpin-loop elements occupying the edges of the icosahedron and connected by single-stranded regions. More recently, Schroeder et al. have combined the results of chemical probing with a novel helix searching algorithm to propose a specific secondary structure for the STMV genome, compatible with the Larson-McPherson model. Here we report an all-atom model of STMV, using the complete protein and RNA sequences and the Schroeder RNA secondary structure. As far as we know, this is the first all-atom model for the complete structure of any virus (100% of the atoms) using the natural genomic sequence.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D002213 Capsid The outer protein protective shell of a virus, which protects the viral nucleic acid. Capsids are composed of repeating units (capsomers or capsomeres) of CAPSID PROTEINS which when assembled together form either an icosahedral or helical shape. Procapsid,Prohead,Capsids,Procapsids,Proheads
D012367 RNA, Viral Ribonucleic acid that makes up the genetic material of viruses. Viral RNA
D055029 Inverted Repeat Sequences Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions. Hairpin Loop Sequence,Inverted Repeat Sequence,Inverted Tandem Repeats,Palindromic Repeat Sequences,Sequence Palindromes,Stem-Loop Sequence,Hairpin Loop Sequences,Inverted Tandem Repeat,Palindrome, Sequence,Palindromes, Sequence,Palindromic Repeat Sequence,Repeat Sequence, Inverted,Repeat Sequence, Palindromic,Repeat Sequences, Inverted,Repeat Sequences, Palindromic,Repeat, Inverted Tandem,Repeats, Inverted Tandem,Sequence Palindrome,Sequence, Hairpin Loop,Sequence, Inverted Repeat,Sequence, Palindromic Repeat,Sequence, Stem-Loop,Sequences, Hairpin Loop,Sequences, Inverted Repeat,Sequences, Palindromic Repeat,Sequences, Stem-Loop,Stem Loop Sequence,Stem-Loop Sequences,Tandem Repeat, Inverted,Tandem Repeats, Inverted
D018360 Crystallography, X-Ray The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) X-Ray Crystallography,Crystallography, X Ray,Crystallography, Xray,X Ray Crystallography,Xray Crystallography,Crystallographies, X Ray,X Ray Crystallographies
D019400 Tobacco mosaic satellite virus A spherical RNA satellite virus which requires an obligatory helper TOBACCO MOSAIC VIRUS for replication. Satellite Tobacco Mosaic Virus,Tobacco Mosaic Virus Satellite
D020836 Protein Structure, Quaternary The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain). Quaternary Protein Structure,Protein Structures, Quaternary,Quaternary Protein Structures

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