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PDB ID Mentions in PubMed Central Article count: 2

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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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"Hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms.

(2008) BMC Struct Biol 8

PubMed: 18312638 | PubMedCentral: PMC2294123 | DOI: 10.1186/1472-6807-8-14

2.00 0.20 59 Oxidoreductase Superoxide Dismutase 31 1SRV A a/b Thermus thermophilus 1.70 1KID 0 a/b Escherichia coli 1.70 0.00 69 Chaperone Groel 32 1UZB A a/b Thermus thermophilus 1.40 1O0A A a/b Hal... bacterium salinarum 1.42 0.02 34 Oxidoreductase 1-Pyrroline-5-Carboxylate Dehydrogenase 33 1V6S A a/b Thermus thermophilus 1.50 16PK 0 a/b Trypanosoma brucei 1.60 0.10 43 Transferase Phosphoglycerate Kinase 34 1V8F A a/b Thermus thermophilus 1.90 1N2E A a/b M. tuberculosis 1.60 0.30 55 Ligase Pantothenate Synthetase 35 1VC4 A a/b Thermus thermophilus 1.80 1PII 0 a/b Escherichia coli 2.00 0.20 37 Lyase Indole-3-Glycerolphosphate Synthase 36 1VCD A a/b Thermus thermophilus 1.70 1SJY A a/b Deinococcus radiodurans 1.39 0.31 34 Hydrolase Ap6a Hydroxylase Ndx1 37 1YYA A a/b Thermus thermophilus 1.60 1MO0 A a/b Caenorhabditis elegans 1.70 0.10 44 Isomerase Triosephosphate Isomerase 38 2PRD 0 a/b Thermus thermophilus 2.00 1SXV A a/b M. tuberculosis 1.30 0.70 51 Hydrolase Inorganic Pyrophosphatase * Optimal growth temperatures are between 50°C and 80°C for thermophiles, and above 80°C for hyperthermophiles Table 2 Hyperthermophilic/Mesophilic (1–38) and Thermophilic/Mesophilic (39–59) pairs in dataset B ID PDB Class Organism Res (Å) PDB Class Mesophile Res (Å) ΔÅ %identity Functional Class Description 1 1A2Z A a/b Thermococcus litoralis 1.73 1AUG A a/b Bacillus amyloliquefaciens 2.00 0.27 37 Peptidase Pyrrolidone Carboxyl Peptidase 2 1A53 0 a/b Sulfolobus solfataricus 2.00 1PII 0 a/b Escherichia coli 2.00 0.00 38 Synthase Indole-3-Glycerolphosphate Synthase 3 1DQI A mainly b Pyrococcus furiosus 1.70 1DFX 0 mainly b Desulfovibrio desulfuricans 1.90 0.20 34 Oxidoreductase Superoxide Reductase 4 1FTR A a+b Methanopyrus kandleri 1.70 1M5S A a+b Methanosarcina barkeri 1.85 0.15 59 Transferase Formyltransferase 5 1DD3 A a/b Thermotoga maritima 2.00 1CTF 0 a/b Escherichia coli 1.70 0.3 69 Ribosomal Ribosomal Protein 6 1G29 1 a/b Thermococcus litoralis 1.90 1B0U A a/b Salmonella typhimurium 1.50 0.40 31 Sugar Binding Malk Protein 7 1HDG O a/b Thermotoga maritima 2.50 1RM4 A a/b Spinacia oleracea 2.00 0.50 56 Oxidoreductase Glyceraldehyde 3 Phosphate Dehydrogenase 8 1HQK A a/b Aquifex aeolicus 1.60 1W19 A a/b Mycobacterium tuberculosis 2.00 0.40 50 Transferase Lumazine Synthase 9 1I4N A a/b Thermotoga maritima 2.50 1PII 0 a/b Escherichia coli 2.00 0.50 34 Lyase Indole-3-Glycerolphosphate Synthase 10 1IOF A a/b Pyrococcus furiosus 2.20 1AUG A a/b Bacillus amyloliquefaciens 2.00 0.20 43 Hydrolase Pyrrolidone-Carboxylate Peptidase 11 1IU8 A a/b Pyrococcus horikoshii 1.60 1AUG A a/b Bacillus amyloliquefaciens 2.00 0.40 45 Hydrolase Pyrrolidone-Carboxylate Peptidase 12 1J0A A a/b Pyrococcus horikoshii 2.50 1TZJ A a/b Pseudomonas sp .

Table 1 Hyperthermophilic/Mesophilic (1–24) and Thermophilic/Mesophilic (25–38) pairs in dataset A* ID PDB Class Organism Res (Å) PDB Class Mesophile Res (Å) ΔÅ %identity Functional Class Description 1 1A2Z A a/b Thermococcus litoralis 1.73 1AUG A a/b Bacillus amyloliquefaciens 2.00 0.27 37 Peptidase Pyrrolidone Carboxyl Peptidase 2 1A53 0 a/b Sulfolobus solfataricus 2.00 1PII 0 a/b Escherichia coli 2.00 0.00 38 Synthase Indole-3-Glycerolphosphate Synthase 3 1DD3 A a/b Thermotoga maritima 2.00 1CTF 0 a/b Escherichia coli 1.70 0.3 69 Ribosomal Ribosomal Protein 4 1DQI A mainly b Pyrococcus furiosus 1.70 1DFX 0 mainly b D. desulfuricans 1.90 0.20 34 Oxidoreductase Superoxide Reductase 5 1FTR A a+b Methanopyrus kandleri 1.70 1M5S A a+b Methanosarcina barkeri 1.85 0.15 59 Transferase Formyltransferase 6 1G29 1 a/b Thermococcus litoralis 1.90 1B0U A a/b Salmonella typhimurium 1.50 0.40 31 Sugar Binding Malk Protein 7 1HQK A a/b Aquifex aeolicus 1.60 1W19 A a/b M. tuberculosis 2.00 0.40 50 Transferase Lumazine Synthase 8 1IU8 A a/b Pyrococcus horikoshii 1.60 1AUG A a/b Bacillus amyloliquefaciens 2.00 0.40 45 Hydrolase Pyrrolidone-Carboxylate Peptidase 9 1J31 A a/b Pyrococcus horikoshii 1.60 1UF5 A a/b Agrobacterium sp .

Publication Year: 2008


Lumazine synthase protein cage nanoparticles as antigen delivery nanoplatforms for dendritic cell-based vaccine development.

(2014) Clin Exp Vaccine Res 3

PubMed: 25003097 | PubMedCentral: PMC4083076 | DOI: 10.7774/cevr.2014.3.2.227

We thank A. M. Seddon for help with transmission electron microscopy and analytical ultracentrifufation studies and G. D. Ruggiero for the generation of computer images Angew Chem Int Ed Engl 2001 40 ... 42 445 11180351 11 Moon H Kim WG Lim S Fabrication of uniform layer-by-layer assemblies with complementary protein cage nanobuilding blocks via simple His-tag/metal recognition J Mater Chem B 2013 1 4504 4510 12 Steinman RM Decisions about dendritic cells: past, present, and future Annu Rev Immunol 2012 30 1 22 22136168 13 Steinman RM Banchereau J Taking dendritic cells into medicine Nature 2007 449 419 426 17898760 14 Han JA Kang YJ Shin C Ferritin protein cage nanoparticles as versatile antigen delivery nanoplatforms for dendritic cell (DC)-based vaccine development Nanomedicine 2014 10 561 569 24262997 15 Trumpfheller C Longhi MP Caskey M Dendritic cell-targeted protein vaccines: a novel approach to induce T-cell immunity J Intern Med 2012 271 183 192 22126373 16 Do Y Koh H Park CG Targeting of LcrV virulence protein from Yersinia pestis to dendritic cells protects mice against pneumonic plague Eur J Immunol 2010 40 2791 2796 20812236 17 Flynn BJ Kastenmuller K Wille-Reece U Immunization with HIV Gag targeted to dendritic cells followed by recombinant New York vaccinia virus induces robust T-cell immunity in nonhuman primates Proc Natl Acad Sci U S A 2011 108 7131 7136 21467219 18 Wang B Zaidi N He LZ Targeting of the non-mutated tumor antigen HER2/neu to mature dendritic cells induces an integrated immune response that protects against breast cancer in mice Breast Cancer Res 2012 14 R39 22397502 19 Trumpfheller C Finke JS Lopez CB Intensified and protective CD4+ T cell immunity in mice with anti-dendritic cell HIV gag fusion antibody vaccine J Exp Med 2006 203 607 617 16505141 20 Wright A Morrison SL Effect of glycosylation on antibody function: implications for genetic engineering Trends Biotechnol 1997 15 26 32 9032990 21 Lampkin BC Levine AS Levy H Krivit W Hammond D Phase II trial of a complex polyriboinosinic-polyribocytidylic acid with poly-L-lysine and carboxymethyl cellulose in the treatment of children with acute leukemia and neuroblastoma: a report from the Children's Cancer Study Group Cancer Res 1985 45 11 Pt 2 5904 5909 2414002 22 Batista-Duharte A Lindblad EB Oviedo-Orta E Progress in understanding adjuvant immunotoxicity mechanisms Toxicol Lett 2011 203 97 105 21392560 Fig. 1 Surface and ribbon diagram representations of AaLS (PDB: 1HQK) looking down the five-fold symmetry axis (A) and clipped view showing the interior space (9 nm interior and 15.4 nm exterior diameters) of the protein cage (B).

Publication Year: 2014