Primary Citation PubMed: 11014183
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PALSSE: a program to delineate linear secondary structural elements from protein structures.
(2005) BMC Bioinformatics 6
PubMed: 16095538 | PubMedCentral: PMC1190160 | DOI: 10.1186/1471-2105-6-202
e, f, g shows cartoon diagrams of chain "J" of "1fjg", prepared using MOLSCRIPT , highlighting β-strand and helix definitions by our program, DSSP, and P-SEA respectively.
We chose an averaged NMR structure "1ahk" and a low-resolution X-ray structure (3.0Å) "1fjg" to show as examples since over-prediction by our method is maximum for such structures.
3e–h are from a low-resolution (3.0Å) X-ray structure (PDB ID: 1fjg, chain "J" [ 30 ]) which has a ferredoxin-like fold made up of two β-α-β units.
Our interpretation of helix and β-strands from PDB files 1ahk and 1fjg (chain "J") by various programs are respectively colored in figs.
Publication Year: 2005
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.
(2006) Biol Direct 1
PubMed: 16545108 | PubMedCentral: PMC1462988 | DOI: 10.1186/1745-6150-1-7
The VAST program [ 40 ] finds ribosomal protein S6 (PDB Entry 1fjg chain F) as the top hit for the C-terminal RMAP domain with P-value 0.039, RMSD 2.6 Å over 64 residues.
Publication Year: 2006
Detecting coevolution in and among protein domains.
(2007) PLoS Comput Biol 3
PubMed: 17983264 | PubMedCentral: PMC2098842 | DOI: 10.1371/journal.pcbi.0030211
Figure 5 marks the coevolving amino acid residues (colored spheres) and the 16S rRNA nucleotides of the tRNA binding sites (colored ribbons) in Thermus thermophilus 30S ribosomal subunit ([ 26... ], PDB id 1fjg).
Publication Year: 2007
Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry.
(2008) Nucleic Acids Res 36
PubMed: 18276647 | PubMedCentral: PMC2275128 | DOI: 10.1093/nar/gkn008
These correspond to the PDB chains 1m8x-A, 1fjg-K, 1fjg-T, 1g1x-B, 1mzp-A, 1sds-C, 1vq8-H, 1b23-P, 1c0a-A, 1f7u-A and 1q2r-A.
Publication Year: 2008
The origin and evolution of the ribosome.
(2008) Biol Direct 3
PubMed: 18430223 | PubMedCentral: PMC2386862 | DOI: 10.1186/1745-6150-3-16
The 16S coordinates are for 1FJG; those in parentheses are for the E. coli , 1GIXstructure.
Equivalent coordinates are in 1FJG .
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.
(2009) Nucleic Acids Res 37
PubMed: 19279186 | PubMedCentral: PMC2691814 | DOI: 10.1093/nar/gkp119
A Mg 2+ -μc in the 16S rRNA of T. thermophilus [PDB entry 1FJG ( 41 )], appears to be disrupted upon ribosomal assembly [PDB entry 2J00 ( 13 )].
Publication Year: 2009
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
PubMed: 19443443 | PubMedCentral: PMC2699532 | DOI: 10.1093/nar/gkp318
( d ) Alignment of bacterial ribosome from E. coli (PDB id: 2qbd, 20 chains, thick backbone) with ribosome of the bacterial species Thermus thermophilus (PDB id: 1fjg, 20 chains, thin backbone).
The structures come from the bacterial ribosome in E. coli (PDB id: 2qbd) and the ribosome of the bacterial species Thermus thermophilus (PDB id: 1fjg); both have 20 protein chains.
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.
(2010) Nucleic Acids Res 38
PubMed: 19906714 | PubMedCentral: PMC2811024 | DOI: 10.1093/nar/gkp956
( B ) Superposition of four X-ray structures in grey (pdb code: 1f7y (tetraloop (TL) 1 and 2), 1i6u, 1fjg).
Publication Year: 2010
Genetic interactions show the importance of rRNA modification machinery for the role of Rps15p during ribosome biogenesis in S. cerevisiae.
(2010) PLoS One 5
PubMed: 20454621 | PubMedCentral: PMC2862742 | DOI: 10.1371/journal.pone.0010472
Obtained using Pymol and PDB #1FJG.
Mutation K42R in ribosomal protein S12 does not affect susceptibility of Mycobacterium smegmatis 16S rRNA A-site mutants to 2-deoxystreptamines.
PubMed: 20700526 | PubMedCentral: PMC2916820 | DOI: 10.1371/journal.pone.0011960
(Protein Data Bank, 1FJG.
Structural modelling PyMol (DeLano Scientific) was used to render the structure of the A-site of 30S ribosomal subunit from T. thermophilus (Protein Data Bank, 1FJG.
Structural signatures of antibiotic binding sites on the ribosome.
PubMed: 20494981 | PubMedCentral: PMC2952860 | DOI: 10.1093/nar/gkq411
Crystallographic structures of T. thermophilus (T.t) and E.coli (E.c) small subunit, and H. marismortui (H.m) and D. radiodurans (D.r) large subunit complexed to antibiotics Index Subunit Antibiotics ... W (Da) Organism PDB Identifier Resolution Refs 1 30S Hygromycin B 527.52 T.t 1HNZ HYG 3.3 Å ( 53 ) 2 30S Pactamycin 558.62 T.t 1HNX PCY 3.4 Å ( 53 ) 3 30S Tetracycline 444.44 T.t 1HNW TAC 1001 3.4 Å ( 53 ) 4 30S Tetracycline 444.44 T.t 1HNW TAC 1002 3.4 Å ( 53 ) 5 30S Tetracycline 444.44 T.t 1I97 TAC 2001 4.5 Å ( 7 ) 6 30S Tetracycline 444.44 T.t 1I97 TAC 2003 4.5 Å ( 7 ) 7 30S Tetracycline 444.44 T.t 1I97 TAC 2004 4.5 Å ( 7 ) 8 30S Tetracycline 444.44 T.t 1I97 TAC 2005 4.5 Å ( 7 ) 9 30S Tetracycline 444.44 T.t 1I97 TAC 2006 4.5 Å ( 7 ) 10 30S Edeine 781.9 T.t 1I95 EDE 4.5 Å ( 7 ) 11 30S Spectinomycin 332.35 T.t 1FJG SCM 3 Å ( 54 ) 12 30S Streptomycin 581.57 T.t 1FJG SRY 3 Å ( 54 ) 13 30S Paromomycinaromomycin 615.63 T.t 1FJG PAR 3 Å ( 54 ) 14 30S Kasugamycin 379.36 T.t 2HHH KSG 1523 3.35 Å ( 57 ) 15 30S Hygromycin B 527.52 E.c 3DF1 HYG 3.5 Å ( 58 ) 16 30S Spectinomycin 332.35 E.c 2QOU SCM 3.93 Å ( 59 ) 17 30S Kasugamycin 379.36 E.c 1VS5 KSG 3.5 Å ( 60 ) 18 30S Gentamicin 449.54 E.c 2QB9 LLL 2356 3.54 Å ( 10 ) 19 30S Gentamicin 449.54 E.c 2QB9 LLL 2357 3.54 Å ( 10 ) 20 30S Gentamicin 449.54 E.c 2QB9 LLL 2357 3.54 Å ( 10 ) 21 30S Neomycin 614.64 E.c 2QAL NMY 3.21 Å ( 10 ) 22 50S Erythromycin 733.93 H.m 1YI2 ERY 2.65 Å ( 56 ) 23 50S Azithromycin 748.99 H.m 1YHQ ZIT 2.4 Å ( 56 ) 24 50S Telithromycin 812.01 H.m 1YIJ TEL 3.4 Å ( 56 ) 25 50S Quinupristin 1022.22 H.m 1YJW SYB 2.9 Å ( 56 ) 26 50S Virginiamycin S 823.89 H.m 1YIT VRS 2.8 Å ( 56 ) 27 50S Virginiamycin M 525.59 H.m 1YIT VIR 2.8 Å ( 56 ) 28 50S Clindamycin 424.98 H.m 1YJN CLY 3 Å ( 56 ) 29 50S Carbomycin 841.98 H.m 1K8A CAI 3 Å ( 35 ) 30 50S Spiramycin 843.05 H.m 1KD1 SPR 3 Å ( 35 ) 31 50S Tylosin 916.1 H.m 1K9M TYK 3 Å ( 35 ) 32 50S Sparsomycin 361.44 H.m 1M90 SPS 2.8 Å ( 55 ) 33 50S Chloramphenicol 323.13 H.m 1NJI CLM 2.55 Å ( 3 ) 34 50S Anisomycin 265.31 H.m 1K73 ANM 3.01 Å ( 3 ) 35 50S Blasticidin S 422.44 H.m 1KC8 BLS 9001 3.01 Å ( 3 ) 36 50S Blasticidin S 422.44 H.m 1KC8 BLS 9002 3.01 Å ( 3 ) 37 50S Homoharringtonine 545.62 H.m 3G6E HMT 2.7 Å ( 61 ) 38 50S Bruceantin 548.58 H.m 3G71 WIN 3.85 Å ( 61 ) 39 50S Tiamulin 493.74 H.m 3G4S MUL 3.2 Å ( 61 ) 40 50S Oxazolidinone 513.52 H.m 3CXC SLD 3 Å ( 62 ) 41 50S Girodazole 190.63 H.m 2OTL GIR 2.7 Å ( 12 ) 42 50S 13-deoxytedanolide 594.73 H.m 2OTJ 13T 2.9 Å ( 12 ) 43 50S Erythromycin 733.93 D.r 1JZY ERY 3.5 Å ( 63 ) 44 50S Clindamycin 424.98 D.r 1JZX CLY 3.1 Å ( 63 ) 45 50S Clarithromycin 747.95 D.r 1J5A CTY 3.5 Å ( 63 ) 46 50S Roxithromycin 837.05 D.r 1JZZ ROX 3.8 Å ( 63 ) 47 50S Chloramphenicol 323.13 D.r 1K01 CLM 3.5 Å ( 63 ) 48 50S Azithromycin 748.99 D.r 1NWY ZIT 1 3.3 Å ( 64 ) 49 50S Azithromycin 748.99 D.r 1NWY ZIT 2 3.3 Å ( 64 ) 50 50S Cethromycin 765.93 D.r 1NWX 773 3.5 Å ( 64 ) 51 50S Telithromycin 812.01 D.r 1P9X TEL 3.4 Å ( 65 ) 52 50S Quinupristin 1022.22 D.r 1SM1 SYB 3.42 Å ( 66 ) 53 50S Dalfopristin 690.85 D.r 1SM1 DOL 3.42 Å ( 66 ) 54 50S Sparsomycin 361.44 D.r 1NJN SPS 3.7 Å ( 67 ) 55 50S Troleandomycin 813.97 D.r 1OND TAO 3.4 Å ( 68 ) 56 50S Tiamulin 493.74 D.r 1XBP MUL 3.5 Å ( 69 ) 57 50S Thiostrepton 1664.89 D.r 3CF5 TXX 3.3 Å ( 21 ) 58 50S Oxazolidinone 337.35 D.r 3DLL ZLD 3.5 Å ( 70 ) 59 50S SB-571519 498.57 D.r 2OGM G19 3.5 Å ( 45 ) 60 50S SB-280080 477.70 D.r 2OGN G80 3.56 Å ( 45 ) 61 50S SB-275833 517.76 D.r 2OGO G34 3.66 Å ( 45 ) 62 50S Rapamycin 914.17 D.r 1Z58 RAP 3.8 Å ( 13 ) 63 50S Josamycin 828.00 D.r 2O44 JOS 3.3 Å ( 71 ) 64 50S RU-69874 972.22 D.r 2O45 RU6 3.6 Å ( 71 ) 65 50S Erythromycylamine 734.96 D.r 2O43 ERN 3.6 Å ( 71 ) Extracting putative pockets in the ribosome The program ‘solvent’ from the 3V package ( http://geometry.molmovdb.org/3v/ ) was applied to identify putative pockets in the ribosome ( 22 ).
Structural characterization of naturally occurring RNA single mismatches.
(2011) Nucleic Acids Res 39
PubMed: 20876693 | PubMedCentral: PMC3035445 | DOI: 10.1093/nar/gkq793
Representation of a U·U mismatch in the 5′ (U)W/ 3′ (U)W pairing, antiparallel, cis orientation with XVI hydrogen bonding pattern (PDB ID 1FJG), which is the most common orient... tion and interaction determined for the most frequently occurring U·U mismatch-nearest neighbor combinations ( 84 ) that were also represented in the PDB.
Representation of an A·C mismatch in the 5′ (A)H/ 3′ (C)W pairing, antiparallel, trans orientation with XXV hydrogen bonding pattern (PDB ID 1FJG)), which is the most common orientation and interaction determined for the A·C mismatch-nearest neighbor combination of .
Representation of a C·U mismatch in the 5′ (C)W/ 3′ (U)W pairing, antiparallel, cis orientation with one_hbond hydrogen bonding pattern (PDB ID 1FJG), which is the most common orientation and interaction determined for the most frequently occurring C·U mismatch-nearest neighbor combinations ( 84 ) that were also represented in the PDB.
Publication Year: 2011
Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: possible misannotation of this tubercle bacilli-hemolysin.
(2011) BMC Struct Biol 11
PubMed: 21443791 | PubMedCentral: PMC3072309 | DOI: 10.1186/1472-6807-11-16
Both, protein structure and function models ( 3HP7 , 1QD7 , 1Q8K , 3DOU , 2PLW , 1FJG , 1EJ0 PDB entries) were compared to the secondary consensus sequence obtained as described above.
Novel base triples in RNA structures revealed by graph theoretical searching methods.
(2011) BMC Bioinformatics 12 Suppl 13
PubMed: 22373013 | PubMedCentral: PMC3278836 | DOI: 10.1186/1471-2105-12-S13-S2
We did not observe any triples that involved all three domains of the T. thermophilus 16S rRNA structure [PDB: 1fjg], although two triples were observed to interface two different domains.
However, in contrast to the high conservation of triples in the large subunit, our alignments for the 16S rRNA sequences, which are otherwise well known to be highly conserved in sequence [ 32 ], showed that only three out of the fifteen triples in T. thermophilus [PDB: 1fjg] are conserved for all three base positions of a triple.
A comparison of the crystal structures of eukaryotic and bacterial SSU ribosomal RNAs reveals common structural features in the hypervariable regions.
(2012) PLoS One 7
PubMed: 22693601 | PubMedCentral: PMC3364965 | DOI: 10.1371/journal.pone.0038203
Materials and Methods The RasMol program  ,  was used for a detailed visual mapping of the base pairs,long-range tertiary contacts, and RNA-protein interactions in the two eukaryotic (PDB IDs ... XZM and 3U5B/3U5C) and one bacterial (PDB ID 1FJG) SSU rRNA crystal structures  ,  .
Publication Year: 2012
Structural analysis of hypothetical proteins from Helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins.
(2012) Int J Mol Sci 13
PubMed: 22837682 | PubMedCentral: PMC3397514 | DOI: 10.3390/ijms13067109
The S4 superfamily includes the Hsp15 protein (PDB code: 1DM9-B), ribosomal small subunit pseudouridine synthase A (PDB code: 1VIO-A), 30S ribosomal protein S4 (PDB code: 1FJG-D), and so on.
Structure of the RNA claw of the DNA packaging motor of bacteriophage ?29.
(2012) Nucleic Acids Res 40
PubMed: 22879380 | PubMedCentral: PMC3479190 | DOI: 10.1093/nar/gks724
( A ) Bulge regions of the 27b and 16S ribosomal RNA of Thermus thermophilus (PDB code 1FJG) are shown.
Of these, a fragment of the 30S ribosomal subunit of Thermus thermophilus containing 16S ribosomal RNA has a bulge structure (PDB code 1FJG; 1441-GGGA-1445:A1460) similar to our 27b RNA ( Figure 6 A).
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.
(2013) Nucleic Acids Res 41
PubMed: 23293000 | PubMedCentral: PMC3575793 | DOI: 10.1093/nar/gks1331
A comparable structure with an A:A:A triad has also been observed in the 30 S ribosomal subunit (PDB id: 1FJG) ( 56 ).
Publication Year: 2013
Evolutionary evidence for alternative structure in RNA sequence co-variation.
(2013) PLoS Comput Biol 9
PubMed: 23935473 | PubMedCentral: PMC3723493 | DOI: 10.1371/journal.pcbi.1003152
The crystal structure is based on PDB ID 1FJG, base-pairs having MI support in the crystal structure above the specified threshold are colored red, while those in grey are below the threshold.
A comparison of structural and evolutionary attributes of Escherichia coli and Thermus thermophilus small ribosomal subunits: signatures of thermal adaptation.
(2013) PLoS One 8
PubMed: 23940533 | PubMedCentral: PMC3734280 | DOI: 10.1371/journal.pone.0069898
Our results show that the largest cavity in T. thermophilus 16S rRNA (structure PDB-id: 1FJG) contains 289.49 Å 3 volume; whereas the largest E. coli 16S rRNA (structure PDB-id: 2AVY) cavity c... ntains 1631.79 Å 3 volume of space.
Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation.
(2013) Bioorg Med Chem 21
PubMed: 23886813 | PubMedCentral: PMC3744816 | DOI: 10.1016/j.bmc.2013.06.056
4.2 Comparison with protein/RNA-streptomycin complex structures The conformation of streptomycin bound to the bacterial 30S ribosomal subunit (its natural target), has been determined to 3.0 &... x000c5; (PDB code 1FJG ) 45,46 and to ∼3.5 Å (PDB codes 4DR3 and 4DR5 –7) in a range of apo - and tRNA-bound states.
An overlay of the coordinates of the highest-resolution structure (PDB code 1FJG ) with the most populated mode conformation in aqueous solution (i.e., the Family 1 linkage conformation) demonstrates that (within error of the crystal structure) the most populated conformational family in aqueous solution is the same as the bioactive conformation ( Fig. 3 ).
(Left) The bioactive conformation of streptomycin (blue) from its co-complex with the 30S ribosome particle (PDB code 1FJG ) is very similar to Family 1 conformational macrostates (the most populated) present in aqueous solution, demonstrating that the bioactive conformation of streptomycin is encoded within its preferred unbound solution conformations.
The highest resolution bioactive conformation (i.e., when streptomycin is bound to the ribosome, PDB code 1FJG ) is shown in blue, lower resolution ones in cyan (PDB codes 4DR3,5–7) and the free crystal structure 57 is in green.
NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions.
(2014) Biochemistry 53
PubMed: 24364590 | PubMedCentral: PMC3906864 | DOI: 10.1021/bi401484a
In one case (PDB code 1FJG), the divalent metal ion forms a cation−π interaction with a cytidine.
Interestingly, in one of these three structures (PDB entry 1FJG), 94 the bound metal ion also forms a cation−π interaction with a cytidine.
Publication Year: 2014
4'-O-substitutions determine selectivity of aminoglycoside antibiotics.
(2014) Nat Commun 5
PubMed: 24473108 | PubMedCentral: PMC3942853 | DOI: 10.1038/ncomms4112
( d ) Superposition of helix 44 of 16S RNA for structures of 30S-compound 1 (green) and 30S-paromomycin (salmon, Protein Data Bank ID code 1FJG); the orientations of A1492 and A1493 that are flipped-o... t from helix 44 are tilted relative to the paromomycin structure.
Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts.
(2014) Nat Methods 11
PubMed: 24584194 | PubMedCentral: PMC3985481 | DOI: 10.1038/nmeth.2876
Motif name PDB a N nt b rmsd-top1 c , d (Å) rmsd-top5 c , e (Å) Known structures Single G:G mismatch 1F5G 6 0.71 0.71 UUCG tetraloop 2KOC 6 0.84 0.84 Tandem GA:AG mismatch 1MIS 8 1.10 ... .10 Tandem UG:UA mismatch 2JSE 8 3.02 2.52 16S rRNA UUAAGU loop 1FJG 8 0.52 0.52 HIV-1 TAR apical loop 1ANR 8 5.86 5.86 tRNA i Met ASL 1SZY 9 3.89 1.35 Conserved SRP internal loop 1LNT 12 0.81 0.81 R2 retrotransposon 4×4 loop 2L8F 12 1.17 1.17 Hepatitis C virus IRES IIa 2PN4 13 3.21 1.48 GAAA tetraloop-receptor 2R8S 15 0.68 0.68 Sc.ai5γ 3-way junction 2LU0 16 3.66 1.74 Blind targets UAAC tetraloop f 4A4R 6 0.94 0.94 UCAC tetraloop f 4A4S 6 1.00 1.00 UGAC tetraloop f 4A4U 6 3.60 1.67 UUAC tetraloop f 4A4T 6 1.72 1.72 Chimp HAR1 GAA loop 2LHP 7 2.88 2.88 Human HAR1 GAA loop 2LUB 7 2.26 2.03 GU:UAU internal loop – g 9 1.37 1.37 tRNA Gly ASL (cuUCCaa) h 2LBL 9 3.28 1.41 tRNA Gly ASL (cuUCCcg) h 2LBK 9 3.42 1.94 tRNA Gly ASL (uuGCCaa) h 2LBJ 9 3.08 2.93 5′-GAGU/3′-UGAG loop 2LX1 12 1.10 1.10 rmsd < 1.50 Å – – 11/23 14/23 rmsd < 2.00 Å – – 12/23 18/23 Additional information and full motif names provided in Supplementary Tables 1 and 3 .
( a ) The crystallographic structure (PDB: 1FJG).
PubMed ID is not available.
Published in 2015
For example, the Thermus thermophilus SSU rRNA structure 1FJG is numbered to match that of Escherichia coli; consequently the nucleotides in the extension of helix 9 are designated sequentially 190A t... rough 190L.
Publication Year: 2015
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs.
(2005) Nucleic Acids Res 33
PubMed: 15745998 | PubMedCentral: PMC552955 | DOI: 10.1093/nar/gki267
Figure 6 Comparison of the graph topologies and 2D and 3D structures of 5S rRNAs ( A and B ) and modules in 16S and 23S rRNAs ( C and D ); (C and D) Two structural (backbone) overlaps of the 5S struct... re (1ffk; gold color) with 16S module (1fjg; blue) and 5S structure with 23S module (1nkw; green) are shown.
From available X-ray structures for Thermus thermophilus 16S rRNA (PDB accession no. 1fjg) ( 50 ) and 23S rRNA from Deinococcus radiodurans (1nkw) and Haloarcula marismortui (1ffk) ( 51 , 52 ), only 5S rRNA motif's matches in domain II of 16S rRNA and domain III of 23S rRNA are relevant; the other three cases are not valid matches in these species.
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