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. 2023 Jun 15;21(6):e3002157. doi: 10.1371/journal.pbio.3002157

Fig 3. Structural similarity between SJR CPs and 30K MPs.

Fig 3

(A) Structures of the SJR CPs homologous to 30K MPs obtained after a DALI search of PDB database, in the upper row highlighted with a blue background. The bottom row shows the jelly-roll region for the selected structures of 30K MP representatives, highlighted with a yellow background. The first structures on the utmost left in the upper and bottom row have the BIDG-CHEF β-strands annotated. The structures are colored using the rainbow scheme from blue (N-terminus) to red (C-terminus). (B) Dendrogram and heatmap of complete linkage clustering of 30K representatives and SJR CPs. The red circles indicated in the top dendrogram, represent bootstrap values ≥90 obtained with R package “pvclust.” The CPs and MPs are indicated in blue and yellow, respectively. Structures of 30K MPs and SJR CPs belong to: BMV, CCMV, FBNSV, STNV, ACMV, AYVV, STMV, SPMV, IPNV, IBDV, BBV, NoV, PrV, NomegaV, BFDV, PCV2, PhMV, TYMV, BYDV, BChV, PVYV, FBPV, RGMoV, RYMV, SBMV, TNV, BPMV, CPMV, FCV, NV, HRV16, SBPV, and CrPV. The newick format of the dendrogram obtained in DALI can be found in S3 Data. ACMV, African cassava mosaic virus; AYVV, ageratum yellow vein virus; BBV, black beetle virus; BChV, beet chlorosis virus; BFDV, beak and feather disease virus; BMV, brome mosaic virus; BPMV, bean pod mottle virus; BYDV, barley yellow dwarf virus; CCMV, cowpea chlorotic mottle virus; CP, capsid protein; CPMV, cowpea mosaic virus; CrPV, cricket paralysis virus; FBNSV, faba bean necrotic stunt virus; FBPV, faba bean polerovirus 1; FCV, feline calicivirus; HRV16, human rhinovirus; IBDV, infectious bursal disease virus; IPNV, infectious pancreatic necrosis virus; MP, movement protein; NomegaV, nudaurelia capensis omega virus; NoV, nodamura virus; NV, Norwalk virus; PCV2, porcine circovirus 2; PDB, Protein Data Bank; PhMV, physalis mottle virus; PrV, providence virus; PVYV, pepper vein yellows virus; RGMoV, ryegrass mottle virus; RYMV, rice yellow mottle virus; SBMV, southern bean mosaic virus; SBPV, slow bee paralysis virus; SJR, single jelly-roll; SPMV, satellite panicum mosaic virus; STMV, satellite tobacco mosaic virus; STNV, satellite tobacco necrosis virus; TNV, tobacco necrosis virus; TYMV, turnip yellow mosaic virus.