Citations in PubMed

Primary Citation PubMed: 11823865 Citations in PubMed

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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On the electrostatic component of protein-protein binding free energy.

(2008) PMC Biophys 1

PubMed: 19351424 | PubMedCentral: PMC2666630 | DOI: 10.1186/1757-5036-1-2

Particular example is tail-associated lysozyme bound to baseplate structural protein GP27 (PDB ID 1k28 ) for which ΔΔG el calculated with Charmm27, e(in) = 1.0 and probe radius 1.4A wa... 261.7 kcal/mol while it was calculated to be 391.1 kcal/mol with Amber98 force field.

Publication Year: 2008


Morphogenesis of the T4 tail and tail fibers.

(2010) Virol J 7

PubMed: 21129200 | PubMedCentral: PMC3004832 | DOI: 10.1186/1743-422X-7-355

Protein Monomer mass (kDa) Oligomeric state in solution Number of monomer copies in the tail Location and remarks Protein Data Bank accession code gp11 23.7 Trimer 18 Wedge, STF # binding interface 1E... 6 gp10 66.2 Trimer 18 Wedge, STF attachment 2FKK gp7 119.2 Monomer 6 Wedge gp8 38.0 Dimer 12 Wedge 1N7Z gp6 74.4 Dimer 12 Wedge 3H2T gp53 23.0 ND* 6 Wedge gp25 15.1 Dimer $ 6 Wedge gp5 63.7 Trimer 3 Hub 1K28 gp27 44.4 Trimer 3 Hub 1K28 gp29 64.4 ND 3 Hub, tail tube, Tape measure gp28 17.3 ND 1‡ Hub; the tip of gp5 needle?

Publication Year: 2010


Type VI secretion system in Pseudomonas aeruginosa: secretion and multimerization of VgrG proteins.

(2011) J Biol Chem 286

PubMed: 21325275 | PubMedCentral: PMC3069435 | DOI: 10.1074/jbc.M110.193045

These structures correspond to Protein Data Bank accession codes 2P5Z and 1K28 .

The predicted VgrG1a structure is very similar to the T4 phage (gp5-gp27) 3 structure reported previously (Protein Data Bank entry 1K28 ).

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

Figure 4 Large β -Strand Rings Can Be Formed by Trimers and Hexamers (A) Trimeric bacteriophage T4 cell puncturing device ( 1k28 , blue).

(C) Single chain of the 1k28 trimer (blue).

Another intriguing detail is the precise match of the three helices at the periphery of the baseplate ring of 1k28 with three of the six helices of the secretion apparatus, 1y12 ( Figure 4 C).

(D) The three chains of the 1k28 trimer colored blue, red, and yellow, respectively.

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.

(C) Superposition of 1k28 and 1y12 .

(E) Cross-section of the 1k28 trimer.

(F) Cross-section of the superimposed 1k28 trimer (blue) and 1 dab monomer (green), with the matching parts in orange and red, respectively.

A quite exceptional match is obtained between the needle of the cell-puncturing device ( 1k28 ) and the structure of pertactin (1dab [ Emsley et al., 1996 ]), a Bordetella pertussis virulence factor ( Figure 5 ).

The matching parts are in orange ( 1k28 ) and red ( 1y12 ).

Pores and Needles Bacteriophage T4 uses an efficient cell-puncturing device ( 1k28 [ Kanamaru et al., 2002; Leiman et al., 2009 ]) for infecting cells.

The match is rather unexpected since the 1k28 needle is a homotrimer, whereas the pertactin needle is built from a single chain that folds into a β helix.

A clear match is obtained between the baseplate ring of 1k28 and the protein secretion apparatus ( 1y12 [ Mougous et al., 2006 ]) from Pseudomonas aeruginosa ( Figure 4 ).

The triangular cross-section ( Figure 5 ) shows that the 1k28 trimer has a perfect three-fold symmetry, whereas the 1dab monomer is rather distorted, with many loops protruding predominantly from one of the three sides of the molecule.

Figure 5 Structurally Equivalent but Topologically Distinct β Helices Can Be Formed by Monomers and Entangled Trimers (A) Bacteriophage T4 cell puncturing device ( 1k28 , blue) and Bordetella pertussis virulence factor pertactin (1dab, green) superimposed with the matching β helix parts in orange and red, respectively.

Publication Year: 2012


DotU and VgrG, core components of type VI secretion systems, are essential for Francisella LVS pathogenicity.

(2012) PLoS One 7

PubMed: 22514651 | PubMedCentral: PMC3326028 | DOI: 10.1371/journal.pone.0034639

According to Phyre2 [36] , the highest similarity to F. tularensis VgrG is exhibited by the C-terminal domain of the tail-associated lysozyme of the T4 bacteriophage (pdb accession 1K28, confidence 99... 8%), whereas HHpred [37] suggests a structural similarity also to the tail spike protein of the bacteriophage P2 (pdb 3AQJ, Prob 84.8, E-value 9), as well as a putative adhesin (pdb 3PET, Prob 88.2, E-value 6.9) present in Bacteroides fragilis .

Publication Year: 2012


PAAR-repeat proteins sharpen and diversify the type VI secretion system spike.

(2013) Nature 500

PubMed: 23925114 | PubMedCentral: PMC3792578 | DOI: 10.1038/nature12453

The structure of the gp5-c1882 complex was solved by molecular replacement with PHASER 19 using a fragment of the gp5-gp27 complex crystal structure containing residues 484-575 of gp5 (PDB ID 1K28) as... a search model 10 .

Publication Year: 2013


TSpred: a web server for the rational design of temperature-sensitive mutants.

(2014) Nucleic Acids Res 42

PubMed: 24782523 | PubMedCentral: PMC4086094 | DOI: 10.1093/nar/gku319

Ts mutant prediction in T4 lysozyme when homology models (identified by their templates) of different accuracies are used Template quality Number of predictions Experimentally validated mutant positio... s PDB:chain Sequence ID (%) DOPE GA341 Sequence Structure Both M6 M102 V103 V149 F153 1pqj:A 90.8 −2.08 1.00 3 (8) 4 (11) 2 (3) Both Both Sequence Structure Structure 1d3n:A 86.1 −1.96 1.00 3 (8) 4 (11) 2 (3) Both Both Sequence Structure Structure 1t8a:A 81.6 −1.65 1.00 3 (8) 4 (13) 2 (3) Both Both Sequence Structure Structure 1cx6:A 79.9 −2.03 1.00 3 (8) 4 (11) 2 (3) Both Both Sequence Structure Structure 1lpy:A 78.8 −1.95 1.00 3 (8) 4 (10) 2 (3) Both Both Sequence Structure Structure 1swz:A 77.5 −2.21 1.00 3 (8) 4 (13) 2 (3) Both Both Sequence Structure Structure 1lwk:A 77.0 −1.74 1.00 3 (8) 4 (12) 2 (3) Both Both Sequence Structure Structure 1swy:A 74.5 −2.22 1.00 3 (8) 4 (12) 2 (3) Both Both Sequence Structure Structure 1sx2:A 72.4 −2.28 1.00 3 (8) 4 (13) 2 (4) Both Both Sequence Structure Structure 1wth:A 43.2 −1.49 1.00 3 (8) 3 (12) 1 (2) Sequence Both Sequence Structure Structure 1k28:A 43.2 −1.43 1.00 3 (8) 5 (15) 3 (5) Both Both Both Structure Structure 2anv:A 24.2 0.54 0.12 3 (8) 1 (11) 1 (2) Sequence Both Sequence 2anx:B 23.9 0.60 0.08 3 (8) 2 (11) 2 (3) Sequence Both Both 2anv:B 23.5 0.49 0.13 3 (8) 2 (11) 2 (3) Sequence Both Both 2anx:A 22.1 0.64 0.13 3 (8) 1 (10) 1 (2) Sequence Both Sequence The number of predictions made by the sequence-based, structure-based or both methods are listed for each of the models with the number of experimentally validated predictions within brackets.

Publication Year: 2014