Citations in PubMed

Primary Citation PubMed: 12093755 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Analysis of the impact of solvent on contacts prediction in proteins.

(2009) BMC Struct Biol 9

PubMed: 19368710 | PubMedCentral: PMC2676287 | DOI: 10.1186/1472-6807-9-22

PFAM ID PDB ID a R (Å) N b % id c L d Ran acc e Acc f R g Opt α h X d dry i Opt Xd α j X d wet | opt α k PF00014 6PTI 1.70 151 33 52 0.096 0.346 3.61 1 9.37 1 11.16 PF0... 705 1AF7 2.00 85 20 57 0.081 0.241 2.65 0.5, 4, 10 6.14 2 7.63 PF00062 5LYZ 2.00 22 46 127 0.043 0.078 1.91 0, 0.5 2.68 0 2.68 PF00018 1BU1 2.60 61 28 56 0.088 0.357 4.06 0.5 12.99 0 12.99 PF03900 1PDA 1.76 21 25 74 0.062 0.237 3.82 2 9.18 0.2 9.99 PF00034 1CTJ 1.10 35 17 89 0.061 0.250 4.10 1 9.13 0.1 10.34 PF01568 1DMR 1.82 88 18 113 0.044 0.050 1.14 0.2, 0.5 10.62 2 12.53 PF00127 8PAZ 1.60 31 29 89 0.055 0.102 1.85 2 0.50 1 4.82 PF01814 2MHR 1.30 295 12 49 0.098 0.400 4.08 0.5, 2 8.39 2 13.14 PF00017 1BMB 1.80 59 28 93 0.058 0.212 3.66 0 – 0.5 5.98 1 8.37 PF01320 1AYI 2.00 45 47 86 0.056 0.233 4.15 0.2 16.04 0 16.04 PF08666 1AME 1.65 171 14 66 0.074 0.273 3.69 0 10.25 0 10.25 PF01337 1A19 2.76 30 25 89 0.065 0.178 2.87 0, 0.1 4.55 0.1 4.72 PF00595 2HB2 2.30 56 19 85 0.062 0.233 3.75 0.5 – 2 10.16 1 11.67 PF00531 1WMG 2.10 92 14 82 0.066 0.250 3.79 0 – 0.5 7.67 0.2 7.95 PF00397 1EG3 2.00 73 32 30 0.143 0.467 3.26 2 – 20 6.59 2 8.81 PF01335 2F1S 1.40 40 21 76 0.072 0.237 3.88 0.1, 0.2 5.66 0.2 5.96 PF00619 1CY5 1.30 61 16 85 0.066 0.209 3.43 0.2 – 2 5.09 2 9.42 PF02213 1SYX 2.35 112 28 58 0.083 0.241 2.91 0.5 – 2 7.37 0.5 7.77 PF05743 1UZX 1.85 28 27 118 0.035 0.068 1.98 0.1 7.22 0 7.22 PF00536 1B4F 1.95 69 28 74 0.076 0.395 5.19 0.2 – 2 15.53 2 16.36 PF03114 1ZWW 2.30 29 19 195 0.021 0.074 3.53 0.2 2.41 20 3.99 PF00169 1NTY 1.70 139 10 112 0.050 0.071 1.43 0, 0.2, 0.5 5.46 2 7.53 PF08416 1WVH 1.50 49 28 132 0.040 0.106 2.65 2, 4 0.53 0.1 1.24 PF01981 1WN2 1.20 69 43 116 0.049 0.172 3.52 0.1 – 0.5 7.63 20 12.38 PF03992 1XBW 1.90 116 15 65 0.068 0.125 1.84 0.5 3.34 0 3.34 PF00907 1H6F 1.70 23 49 183 0.032 0.033 1.03 0 – 20 3.30 2 6.03 PF02237 1WPY 1.60 47 21 48 0.094 0.167 1.77 0.5 – 2 -2.83 0.5 0.22 PF08031 2AXR 1.98 64 34 34 0.135 0.235 1.74 0.1, 0.2 -0.05 2 3.37 PF02861 1K6K 1.80 165 21 51 0.098 0.440 4.49 1, 4, 10, 20 9.55 20 13.21 PF02834 1VGJ 1.94 106 14 85 0.048 0.119 2.48 4 – 20 -0.51 4, 10 3.21 PF01423 1KQ1 1.55 128 23 60 0.079 0.167 2.11 0.2, 0.5 5.78 0.1, 0.2 7.14 PF01472 1AS0 1.80 106 24 78 0.058 0.128 2.21 1 – 20 3.57 2, 4 11.45 PF01909 1NO5 1.80 119 14 91 0.059 0.133 2.26 0.1 – 1 4.97 0.2 6.01 PF09261 1R34 1.95 79 31 78 0.069 0.205 2.97 0.1, 0.2 4.87 0.1 6.64 PF01315 1VLB 1.28 28 19 117 0.041 0.207 5.05 1, 2 7.70 2 10.28 PF04545 1KU3 1.80 128 31 54 0.096 0.370 3.86 0, 0.1, 1, 10, 20 12.37 10, 20 12.76 PF00984 1MV8 1.55 24 17 98 0.048 0.184 3.83 0.5 – 20 8.27 0.2 9.78 PF01658 1U1I 1.90 20 31 105 0.049 0.096 1.96 0.1 – 20 1.93 0.5 6.28 PF00745 1GPJ 1.95 34 23 99 0.048 0.100 2.08 0.1 – 0.5 3.17 0.1 4.17 PF03099 1WNL 1.60 65 14 117 0.043 0.121 2.81 0 13.7 0.2 14.20 PF01985 1JO0 1.37 50 23 84 0.064 0.167 2.60 0 – 0.2 6.96 0 6.96 PF08436 1Q0Q 1.90 77 57 94 0.049 0.213 4.34 0 – 0.1 6.91 10 10.15 PF02881 1JPN 1.90 52 19 85 0.063 0.119 1.89 0 – 20 3.94 2 5.78 PF01966 1YNB 1.76 158 12 91 0.057 0.333 5.85 0 – 0.2 -0.79 2 2.20 PF00191 1YII 1.42 178 28 66 0.076 0.273 3.59 0 – 0.2 -0.35 10 1.05 PF00317 1XJE 1.90 79 23 90 0.056 0.178 3.17 0.5 – 2 10.01 0.5 13.16 PF00046 1PUF 1.90 184 37 60 0.082 0.333 4.07 1, 2 6.07 2 8.60 PF00077 5FIV 1.90 48 27 108 0.049 0.093 1.89 2 -1.37 1 3.63 PF00042 1ECN 1.40 73 18 101 0.046 0.163 3.56 1, 2 6.89 2 7.19 a PDB ID; b Number of sequences; c Average sequences pairwise similarity (%); d Reference sequence length; e Random accuracy; f Accuracy for optimal α ; g Improvement ratio over random prediction for optimal α ; h Values for α = 0; i α corresponding to the highest accuracy; j α corresponding to the highest X d ; k X d highest value.

Publication Year: 2009


Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq.

(2011) Nucleic Acids Res 39

PubMed: 21330354 | PubMedCentral: PMC3113564 | DOI: 10.1093/nar/gkq1346

Since then 13 unique structures of Hfq-proteins from seven different organisms have been deposited in the Protein Data Bank [ S. aureus (Hfq Sa ; amino acids 1–77) 1KQ1, 1KQ2 ( 21 ); E. coli (... fq Ec ; amino acids 1–72) 1HK9 ( 22 ), 3GIB (amino acids 2–69) ( 23 ); Pseudomonas aeruginosa (Hfq Pae ; amino acids 1–82) 1U1T, 1U1S ( 24 ), 3M4G, 3INZ ( 25 ); Methanococcus jannaschii (Hfq Mj ; amino acids 1–71) 2QTX ( 26 ); Synechocystis sp.

Publication Year: 2011


Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.

(2012) Nucleic Acids Res 40

PubMed: 22053080 | PubMedCentral: PMC3287200 | DOI: 10.1093/nar/gkr892

SaHfq (PDB ID: 1KQ1) is shown in magenta, SaHfq–AU 5 G (PDB ID: 1KQ2) in red, EcHfq (PDB ID: 1HK9) in cyan, EcHfq–poly(A) (PDB ID: 3GIB) in blue and P. aeruginosa Hfq (PDB ID: 1U1S) in... orange.

Publication Year: 2012


Crystal structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.

(2012) PLoS One 7

PubMed: 22615807 | PubMedCentral: PMC3355152 | DOI: 10.1371/journal.pone.0036768

Archaeoglobus fulgidus Sm1 protein (AF-Sm1) (PDB code 1I4K); Pyrococcus abyssi Sm1 (PA-Sm1) (PDB code 1M8V); Homo sapiens Sm complex (HS-Sm) (PDB code 2Y9A); Staphylococcus aureus Hfq (SA-Hfq) (PDB co... e 1KQ1).

Publication Year: 2012


Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.

(2012) Nucleic Acids Res 40

PubMed: 22965117 | PubMedCentral: PMC3505971 | DOI: 10.1093/nar/gks809

Structure determination and refinement The structure was solved by molecular replacement using Phaser ( 54 ) and one hexamer of the Hfq apo structure from S. aureus (PDB code: 1KQ1) as the search mode... .

The structure of the complex was solved by molecular replacement using the apo Sa Hfq crystal structure (PDB ID code 1KQ1) as the search model and refined to R work and R free values of 19.6% and 25.9%, respectively, to 2.20 Å resolution ( Table 1 ).

Publication Year: 2012


Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.

(2013) PLoS One 8

PubMed: 23326305 | PubMedCentral: PMC3543421 | DOI: 10.1371/journal.pone.0049044

The N-terminal Zinc finger (ZF) domain of the plasmid proteins is aligned with the ZF domain of the human zinc-fingers and homeoboxes 1 protein (PDB ID: 2GHF), while the C-terminal domain is aligned w... th the Hfq-like proteins from Methanocaldococcus jannaschii (PDB ID: 2QTX) and Staphylococcus aureus (PDB ID: 1KQ1).

Publication Year: 2013


Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function.

(2013) RNA Biol 10

PubMed: 23579284 | PubMedCentral: PMC3710371 | DOI: 10.4161/rna.24538

Representing even greater sequence divergence, the Sm fold of S. aureus Hfq (PDB 1KQ1; blue) and an Sm-like fold in the membrane channel MscS (PDB 2VV5; red) are shown superimposed in ( D ).

Publication Year: 2013