Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Geminiviruses: a tale of a plasmid becoming a virus.

(2009) BMC Evol Biol 9

PubMed: 19460138 | PubMedCentral: PMC2702318 | DOI: 10.1186/1471-2148-9-112

(A) Pseudo-atomic models of the CPs of Panicum streak virus (Mastre; red), Mesta yellow vein mosaic virus (Begomo; green), Horseradish curly top virus (Curto; orange) and Tomato pseudo-curly top virus... (Topocu; cyan) are compared to the atomic model of the CP of Satellite tobacco necrosis virus (STNV; blue; [PDB: 2buk ]).

The secondary structure determined from the X-ray structure of STNV CP [PDB: 2buk ] is shown above the alignment with α helices, β strands, and turns represented by red rectangles, blue arrows, and yellow bulges, respectively.

Of the 184 STNV CP amino acid residues for which structural information is available [PDB: 2buk ], 69.1% had corresponding amino acids in at least one of the four geminiviral CP sequences (75 identical and 52 similar residues) (Fig.

Publication Year: 2009


On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas.

(2011) BMC Evol Biol 11

PubMed: 21711564 | PubMedCentral: PMC3154185 | DOI: 10.1186/1471-2148-11-185

Table 2 Amino acid similarities and identities of some protein sequences deduced from entries of metagenomic study with selected geminivirus CPs Alignment Query sequence Most similar geminivirus CP Id... ntity Similarity length JCVIPEP1105104354663 Q5UAE8 Indian cassava mosaic virus 23.4 39.7 250 JCVIPEP1105107973141 A7UGA6 Sweet potato leaf curl virus 22.4 36.6 183 JCVIPEP1105096364985 A7UGA6 Sweet potato leaf curl virus 22.8 37.6 250 JCVIPEP1105092295201 C7TPA7 Mung bean yellow mosaic India virus 27.3 44.6 139 JCVIPEP1105092294601 Q645H3 Corchorus yellow vein virus 18.5 32.4 222 JCVIPEP1105092292339 Q19LG2 Tomato golden mottle virus 27.6 42.9 217 SNTV (PDBID: 2BUK ) Q4LAS1 Wheat dwarf virus 18.7 32.2 267 The amino acid similarities and identities of the SNTV CP is also included for comparison.

Publication Year: 2011


Detection of spatial correlations in protein structures and molecular complexes.

(2012) Structure 20

PubMed: 22483118 | PubMedCentral: PMC3320710 | DOI: 10.1016/j.str.2012.01.024

The capsids of 2buk and 1vb4 are both constructed from 60 identical subunits that assemble to the T  = 1 variant of the virus particles ( Caspar and Klug, 1962; Erickson et al., 1985 )...

Figure 8 Capsids of Satellite Tobacco Necrosis Virus ( 2buk ) and Sesbania Mosaic Virus ( 1vb4 ) Have Structural Correlations on the Monomer and Pentamer Level (A) Superposition of the monomers of 2buk (chain A, blue) and 1vb4 (chain A, green), with the matching parts in orange and red, respectively.

In fact, the pentamers of 2buk and 1vb4 can be superimposed as a whole where the β -sandwiches in the pentamers attain similar location and orientation ( Figure 8 B).

(B) Superposition of 2buk and 1vb4 pentamers (coloring as in (A)).

(C) The virus capsid of 2buk as in (B), with an additional adjacent pentamer shown as cartoons.

Table 1 Parameters of Structure Alignments Figure Query Target T L Q C T C S S r E r I s P 1 A 3izx ,A 3iyl ,W b 216 17 20 180 2.97 3.09 14 0 1 B 3izx ,A 3iyl ,W b 139 11 13 118 2.84 2.94 14 0 1 C 3izx ,A 3iyl ,W c 634 49 60 380 5.01 5.59 12 0 2 A 1hxm ,AB 3qcv ,HL b 223 51 51 203 2.12 2.21 25 0 2 B 1hxm ,AB 3qcv ,HL b 179 41 41 158 2.47 2.56 25 0 3 AB 2i9p ,ABCD 3fwn ,AB c 641 55 69 497 3.53 3.83 19 1 3 AC 2i9p ,ABCD 3i83 ,AB c 406 35 68 294 3.97 4.28 12 1 3 BC 3fwn ,AB 3i83 ,AB c 260 28 44 178 4.31 4.87 13 2 4 C 1k28 @1 1y12 @1 b 339 12 35 289 2.79 2.92 8 0 5 A 1k28 @1 1dab,A c 321 12 60 243 3.69 3.95 10 0 6 A 2pol @1 1plq @1 c 645 83 88 549 2.81 2.94 10 0 6 C 1plq ,A(1:127) 1plq ,A(128:258) b 114 87 90 103 2.21 2.30 14 0 6 D 1plq ,A(1:127) 2gia ,A(72:217) b 97 72 76 85 2.60 2.70 11 5 7 A 3bkn ,A 2za6 ,A b 152 89 94 136 2.33 2.42 16 0 7 B 3bkn @1 2za6 @1 c 3649 89 94 3202 2.53 2.61 17 0 8 A 2buk ,A 1vb4 ,A c 115 59 63 94 3.13 3.27 4 0 8 B 2buk @1,Aaxyz 1vb4 @1,Aaxyz c 354 36 38 252 4.09 4.37 7 0 Figure, the respective figure and panel; Query, name of the query structure consisting of the PDB code and chain identifier(s) with optional residue numbers in parentheses (from N to C terminus), where the @ sign and the associated number refer to the biological unit as defined in the respective PDB file; Target, name of the target structure (same encoding rules as for the query); T , alignment type (basic, b, or composite, c); L , alignment length; Q c , query cover; T c , target cover; S , similarity; Sr , average distance error; E r , root-mean-square error; I s , fraction of pairs of identical residues; P , number of permutations.

For example, satellite tobacco necrosis virus, a single-stranded RNA virus, forms a capsid containing a total of 11,040 amino acid residues ( 2buk , resolution 2.45 Å [ Jones and Liljas, 1984 ]).

Publication Year: 2012


Virus capsid dissolution studied by microsecond molecular dynamics simulations.

(2012) PLoS Comput Biol 8

PubMed: 22589708 | PubMedCentral: PMC3349721 | DOI: 10.1371/journal.pcbi.1002502

System preparation The starting structures were prepared from the X-ray crystal structure of the coat protein of STNV (PDB ID: 2buk) [2] .

Publication Year: 2012


Evolutionary and molecular aspects of Indian tomato leaf curl virus coat protein.

(2012) Int J Plant Genomics 2012

PubMed: 23304121 | PubMedCentral: PMC3529866 | DOI: 10.1155/2012/417935

Remote-based homology modeling using Phyre provided a model based on the Nucleoplasmin-like/viral protein (viral coat and capsid proteins) as folding unit (PDB ID: 2BUK chain A; structure of satellite... tobacco necrosis virus after crystallographic refinement at 2.5 Å resolution) [ 48 ] derived from satellite virus with a confidence of 97.3.

Publication Year: 2012


Sequence-specific, RNA-protein interactions overcome electrostatic barriers preventing assembly of satellite tobacco necrosis virus coat protein.

(2013) J Mol Biol 425

PubMed: 23318955 | PubMedCentral: PMC3593212 | DOI: 10.1016/j.jmb.2013.01.004

The CP has a backbone r.m.s.d. of 0.138 Å compared to the virion [Protein Data Bank (PDB) entry 2BUK ] 22 and 0.271 Å compared to the VLP containing the mRNA (PDB entry... 3S4G ).

Publication Year: 2013


High-resolution structure of viruses from random diffraction snapshots.

(2014) Philos Trans R Soc Lond B Biol Sci 369

PubMed: 24914154 | PubMedCentral: PMC4052863 | DOI: 10.1098/rstb.2013.0326

For the STNV (PDB designation: 2BUK) used here, this corresponds to atomic resolution (0.2 nm).

Publication Year: 2014