Primary Citation PubMed: 10937989
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Automated extraction and classification of RNA tertiary structure cyclic motifs.
(2006) Nucleic Acids Res 34
PubMed: 16679452 | PubMedCentral: PMC1458283 | DOI: 10.1093/nar/gkl120
MATERIALS AND METHODS PDB structure The 2.4 Å resolution X-ray crystal structure of Haloarcula marismortui LSU ( 1 ) (PDB code 1FFK) was obtained from the PDB ( 19 ).
Publication Year: 2006
Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome.
(2006) PLoS Comput Biol 2
PubMed: 16789821 | PubMedCentral: PMC1523309 | DOI: 10.1371/journal.pcbi.0020098.eor
For all simulations of ribosome-mediated synthesis and folding, the structural model of the large ribosomal subunit solved by Ban et al. was used (pdb file 1FFK; [ 53 ]) and aligned su... h that the exit of the ribosomal tunnel was directed along the − x direction, with the peptidyltransferase active site located near the origin of the coordinate frame.
Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analyses.
(2007) Nucleic Acids Res 35
PubMed: 17308345 | PubMedCentral: PMC1865052 | DOI: 10.1093/nar/gkm065
Molecular modelling of TCS–rRNA complex The coordinates of the SRL were obtained from the crystal structure of the large ribosomal subunit from Haloarcula marismortui (PDB code: 1FFK) ( 32 ), ... nd the coordinates of TCS were obtained from the crystal structure of TCS complexed with adenine (PDB code: 1MRJ).
Publication Year: 2007
The Croonian lecture 2006. Structure of the living cell.
(2008) Philos Trans R Soc Lond B Biol Sci 363
PubMed: 17255009 | PubMedCentral: PMC1955230 | DOI: 10.1098/rstb.2006.1960
( d ) The large subunit of the ribosome (PDB accession code 1ffk) is composed of two strands of RNA (shown as grey and brown wire models) and many different protein chains, shown in blue.
Publication Year: 2008
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.
(2008) Nucleic Acids Res 36
PubMed: 17921499 | PubMedCentral: PMC2238875 | DOI: 10.1093/nar/gkm786
The encoding and searching concept of the RNA FRABASE presented for the Haloarcula marismortui 5S rRNA structure (PDB code 1FFK).
Clicking ‘show coordinates’ button gives access to the fragment(s) coordinates in the PDB-format which can be saved and downloaded for direct visualization at the client site as exemplified by the kissing loop motif structure (example 6, PDB ID 1FFK) using e.g. PyMol software ( 32 ).
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes.
PubMed: 18252772 | PubMedCentral: PMC2330231 | DOI: 10.1093/nar/gkm1171
The results indicate that the C1049–G2751 pair participates in the interaction between the GAR and domain VI of 23S rRNA, although other non-Watson–Crick interactions are also observed... around the C1049–G2751 pair in the five crystal structures of the large subunit reported so far: C1110–G2751, A1048–G2751, A1050–G2751, A1050–C2752 and G1051–C2752 (PDB; 1FFK, 1NKW, 2AWB, 2AW4 and 1VSA).
Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha) atoms.
(2009) PLoS One 4
PubMed: 19214247 | PubMedCentral: PMC2641018 | DOI: 10.1371/journal.pone.0004476
PDB ID Description 1ffk Ribosomal unit 2akh SECYEG ribosomal unit 2esg Complex of IgA and serum albumin 2bcw Ribosomal protein 1xi4 Clathrin coat Discussion An approach has been developed to identify ... he buried and exposed residues in proteins solely based on the positions of Cα atoms.
Publication Year: 2009
Frequency and isostericity of RNA base pairs.
(2009) Nucleic Acids Res 37
PubMed: 19240142 | PubMedCentral: PMC2673412 | DOI: 10.1093/nar/gkp011
Selecting a reduced-redundancy set of PDB files for analysis The RNA-containing 3D structures deposited with the PDB contain multiple versions of some RNA structures (e.g. 1ffk, 1jj2 and 1s72 are all ... D structures of the H. marismortui 23S rRNA).
Transcriptional down-regulation and rRNA cleavage in Dictyostelium discoideum mitochondria during Legionella pneumophila infection.
PubMed: 19492077 | PubMedCentral: PMC2683564 | DOI: 10.1371/journal.pone.0005706
(B) LSU rRNA cleavage sites (red) mapped onto the three-dimensional structure of the Haloarcula marismortui mitochondrial ribosome (pdb 1ffk).
The high-resolution ribosome crystal structure of the halobacterium Haloarcula marismortui was used as a reference model to map D. discoideum mitochondrial LSU rRNA structure in three-dimensions, using PDB 1FFK coordinates  ,  .
FASTR3D: a fast and accurate search tool for similar RNA 3D structures.
PubMed: 19435878 | PubMedCentral: PMC2703968 | DOI: 10.1093/nar/gkp330
For the purpose of demonstration, we selected a fragment from the large subunit of the ribosome in Haloarcula marismortui (PDB ID: 1FFK, chain: 0, nucleotide number: 2558–2575) and applied its... sequence (GGGGCUGAAGAAGGUCCC) to RNA FRABASE (with default parameters) and our FASTR3D (with searching frequently occurring true secondary structures and without matching the query sequence).
Classification and energetics of the base-phosphate interactions in RNA.
PubMed: 19528080 | PubMedCentral: PMC2731888 | DOI: 10.1093/nar/gkp468
Selecting a reduced-redundancy set of PDB files for analysis The RNA-containing 3D structures deposited with the PDB contain multiple versions of some RNA structures (e.g. 1ffk, 1jj2 and 1s72 are all ... D structures of the Haloarcula marismortui 23S rRNA).
The dimeric proto-ribosome: Structural details and possible implications on the origin of life.
(2009) Int J Mol Sci 10
PubMed: 19742176 | PubMedCentral: PMC2738903 | DOI: 10.3390/ijms10072921
In the high resolution structures of the modern ribosome (PDB codes 1FFK, 1NKW, 2AW4), metal ions are found near the single stranded segments of the C-loop, comprising the core unit elbow, but none ar... involved in the dimer-forming interactions between the two core units.
Ion-induced folding of a kink turn that departs from the conventional sequence.
PubMed: 19783814 | PubMedCentral: PMC2790904 | DOI: 10.1093/nar/gkp791
The structure of Kt-7 was taken from the H. marismortui 50S ribosomal subunit, PDB file 1FFK ( 30 ).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
(2010) Nucleic Acids Res 38
PubMed: 19952067 | PubMedCentral: PMC2831300 | DOI: 10.1093/nar/gkp1057
Another distinction between the two models is in the source of the X-ray structures used for the refinement: Gao et al. , 2003 ( 67 ) combined the 50S structure from H.m. (PDB code 1ffk) with the 30S ... tructure from T.t. (PDB code 1ibl), while Gao et al. , 2009 ( 66 ) used the recent (2005) 70S X-ray structure from E.c. [PDB code: 30S: 2avy/50S: 2aw4 ( 23 )].
Publication Year: 2010
Integration of open access literature into the RCSB Protein Data Bank using BioLit.
(2010) BMC Bioinformatics 11
PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220
of Articles 1JJ2 Large Ribosomal Subunit 27 1J5E 30S Ribosomal Subunit 19 1FFK Large Ribosomal Subunit 19 1LMB Lambda Repressor 19 1AAY Zinc Finger 17 1TSR P53 16 1F88 Rhodopsin 15 1BRS Barnase/Barsta... complex 14 The open access literature for RCSB PDB entries is available from the Literature tab for each structure entry at http://www.rcsb.org .
Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases.
PubMed: 20702420 | PubMedCentral: PMC3001072 | DOI: 10.1093/nar/gkq700
One other example of A–A pairing is found within the ribosome model (pdb code 1FFK) ( 35 ), in which both residues are in the anti conformation and interact with their Watson–Crick edg... s within an irregular double-stranded structure.
Structural characterization of naturally occurring RNA single mismatches.
(2011) Nucleic Acids Res 39
PubMed: 20876693 | PubMedCentral: PMC3035445 | DOI: 10.1093/nar/gkq793
For example, the crystal structure of the large ribosomal subunit of Haloarcula marismortui has been solved unbound (PDB I.D. 1ffk) and bound (PDB I.D. 1n8r) to antibiotics.
Publication Year: 2011
RNA and protein 3D structure modeling: similarities and differences.
(2011) J Mol Model 17
PubMed: 21258831 | PubMedCentral: PMC3168752 | DOI: 10.1007/s00894-010-0951-x
Fragments for the assembly of RNA structure were taken from the large ribosomal subunit of Haloarcula marismortui (PDB code: 1ffk).
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
A comparison of triples in four 23S rRNA structures available ( H. marismortui , D. radiodurans , E. coli , T. thermophilus ; PDB: 1ffk, 1nkw, 2awb, 2j01 respectively) and using the H. marismortui str... cture as a reference, shows that 21 out of the 28 triples are also conserved in the other three structures.
These include a triple [C2104.A2485.C2536; PDB: 1ffk] [ 1 ] that was also found to be structurally conserved in the structural alignments and is also conserved in all the sequences aligned.
Structural comparisons of T. thermophilus [PDB: 2j01], E. coli [PDB: 2awb] and D. radiodurans [PDB: 1nkw] to the H. marismortui [PDB: 1ffk] structure were carried out using least squares superposition on the phosphate backbone atoms by the program LSQKAB [ 21 ] from the CCP4 suite [ 22 ].
IM2 Crenarchaeota; Thermoprotei GenBank: NC_003364 Nanoarchaeum equitans Kin4-M Nanoarchaeota GenBank: NC_005213 Haloarcula marismortui Euryarchaeota; Halobacteria PDB: 1ffk Results Searching for structural patterns with graph theory NASSAM [ 17 ], a graph theoretical search engine, was used to screen a nucleic acid database for matches to the 840 patterns derived from the NAIL database and a further 102 from our own procedure (see Additional File 1 Figure S1).
This includes U1371.A2054.U2648 [PDBID 1ffk], which, as discussed earlier, links domains III, IV and V, although the other ten triples do not participate in any inter-domain interactions.
Figure 5 Stereo diagrams showing the eleven triples that approach the polypeptide exit tunnel in H. marismortui 23S rRNA (PDB: 1ffk).
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.
(2012) Nucleic Acids Res 40
PubMed: 22661578 | PubMedCentral: PMC3394293 | DOI: 10.1093/nar/gks513
We were unable to perform direct comparisons between MC-annotate and NASSAM on larger structures such as the rRNA subunits (e.g. 1FFK and 3U5D) as the MC-annotate server does not at present accept suc... large files for analysis, so in the examples below we focus on smaller RNA structures.
A NASSAM search using the Haloarcula marismortui 23S rRNA subunit (PDB ID: 1FFK) as input can quickly provide a snapshot showing that there are at least 13 occurrences of the various tetraloops in the structure ( Figure 2 A).
This includes the ribosomal subunits from prokaryotes (such as PDB ID: 1FFK) ( 28 ) and eukaryotes (such as PDB ID: 3U5D) ( 29 ).
Snapshots of NASSAM output showing ( A ) the results of a GNRA tetraloop search for the H. marismortui 23S rRNA structure (PDB ID: 1FFK) in the left panel with the selected GNRA tetraloop hits viewed relative to the whole structure in a Jmol window in the right panel; ( B ) the results listing the hits to A-minor motifs in the structure of a bacterial ribonuclease P (PDB ID: 3Q1R) in the left panel and a close up examination in Jmol of one selected hit (C85.A232.G263).
Publication Year: 2012
Automated 3D structure composition for large RNAs.
PubMed: 22539264 | PubMedCentral: PMC3413140 | DOI: 10.1093/nar/gks339
The 3D structure of this RNA molecule is known (PDB 1FFK), but the secondary structure is difficult to access solely in silico .
On the left: superposition of the best 3D model (purple) generated from the secondary structure determined in this work, using the RNAstructure software ( 36 ) and the SHAPE chemical structure probing ( 37 ) data, over the X-ray structure (PDB 1FFK; blue).
Integrating chemical footprinting data into RNA secondary structure prediction.
(2012) PLoS One 7
PubMed: 23091593 | PubMedCentral: PMC3473038 | DOI: 10.1371/journal.pone.0045160
If correct, this is a remarkable feat, given that the size of the HIV-1 genome is generally just under 10,000 nt (see http://www.hiv.lanl.gov ), hence several times larger than the ribosome, whose cry... tal structure was only determined after years of painstaking work (the large unit, PDB code 1FFK  , of the ribosome of Haloarcula marismortui consists of a 23S chain of length 2,922 nt and a 5S chain of 122 nt).
Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.
(2013) Nucleic Acids Res 41
PubMed: 23222135 | PubMedCentral: PMC3553981 | DOI: 10.1093/nar/gks1259
Structure-based sequence alignments of the conserved rRNA core were constructed using Sequence to Structure (S2S) ( 27 ) based on X-ray structures of the small ribosomal subunit of Thermus thermophilu... for the 16S rRNA [Protein Data Bank (PDB) code 1fjf] ( 28 ) and the large ribosomal subunit of H. marismortui for the 23S and 5S rRNAs (PDB 1ffk) ( 14 ).
Publication Year: 2013
Computational prediction of associations between long non-coding RNAs and proteins.
(2013) BMC Genomics 14
PubMed: 24063787 | PubMedCentral: PMC3827931 | DOI: 10.1186/1471-2164-14-651
Table 1 Complexes used in the training set Organism Complex ID (PDB database) Haloarcula marismortui 1FFK, 1JJ2 Thermus thermophiles 1GIY, 3HUW, 3I8I Deinococcus radiodurans 1J5A, 2ZJP Escherichia col... 1P85, 2GYA Bos Taurus 2FTC Mus musculus 2R8S Neurospora crassa 2RKJ Canis lupus familiaris 2ZKQ, 2ZKR Spinacia oleracea 3BBN, 3BBO Homo sapiens 3CW1 Thermomyces lanuginosus 3JYV After collecting RNA–protein pairs, a criterion is needed to determine whether a pair is interactive or non-interactive.
Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.
(2014) Nucleic Acids Res 42
PubMed: 24121683 | PubMedCentral: PMC3902895 | DOI: 10.1093/nar/gkt800
All computed interactions are reported with the corresponding PDB code and resolution, of the selected crystal structure Motif Occurrency Interaction PDB; Biomolecule Resolution (Å) Crystallog... aphic G:C motif GCC tWW/tSW 9 G15:C48:C20 1H3E; tRNA Tyr 2.90 W:W trans GCU tWW/Intermediate-O4(U) 10 G:515:C548:U520 1N78; tRNA Glu 2.10 W:W trans GCH2U(rG) tWW/tSW 1 G15:C48:H2U20A:G20B 1SER;tRNA Ser 2.90 W:W trans GrCrG tWW/cSS 74 G430:C234:G219 3uz2; 23S rRNA 2.80 W:W trans GGCU(i) tHS/tWW/tWW 17 G1371:G1360:C2214: U2210 1VS8; 23S rRNA 3.50 W:W trans GGCU(ii) tHS/tWW/tWW 5 G1371:G1360:C2214: U2210 3OAS; 23S rRNA 3.25 Ww/Bs trans GGCU(iii) tHS/tWW/tWW 8 G1371:G1360:C2214: U2210 2AW4; 23S rRNA 3.46 Ww/Bw trans GC tWW/wc 160 G15:C48:w916 1EVV; tRNA Phe 2.00 W:W trans GC tWW/wa 82 G1873:C1856:w9741 1YIJ; 23S rRNA 2.60 W:W trans GC tWW/wcwa 68 G15:C48:w104:w121 1EHZ; tRNA Phe 1.93 W:W trans GC tWW/OP1 269 G2564:C2510:PO1 2508 1FFK; 23S rRNA 2.40 W:W trans GC tWW/OP1wc 34 G2564:C2510:PO1(C2508)w3705 3CCL; 23S rRNA 2.90 W:W trans QM calculations A density functional theory approach, based on the hybrid B3LYP functional as implemented in the gaussian09 package ( 47–49 ) and the cc-pVTZ basis set ( 50 ), was used for all geometry optimizations, both in the gas phase and in water, modeled with the continuum polarizable model C-PCM ( 51 , 52 ).
Motifs (a–e) from PDBs 1EVV, 1YIJ, 1EHZ, 1FFK and 3CCL, respectively.
Publication Year: 2014
Purification of the cystic fibrosis transmembrane conductance regulator protein expressed in Saccharomyces cerevisiae.
(2014) J Vis Exp
PubMed: 24893839 | PubMedCentral: PMC4181556 | DOI: 10.3791/51447
There is no obvious polyHis sequence in the L3 protein, but examination of its 3D structure when bound to the ribosome (PDB = 1FFK) shows that the folded L3 subunit has a potential polyHis cluster.
The K-turn motif in riboswitches and other RNA species.
(2014) Biochim Biophys Acta 1839
PubMed: 24798078 | PubMedCentral: PMC4316175 | DOI: 10.1016/j.bbagrm.2014.04.020
K-turn PDB − 1n: 2b/Å 2b·2n pair/Å O–N3 O–N1 N2–N7 N3–N6 2b·2n N3 class Kt-7 H. m. (free RNA) 4C4O 2.5 2.7 3.0 A·... G Box C/D 1RLG 2.8 2.9 3.1 A·G U4 snRNA 1E7K 3.2 2.7 3.1 A·G Cyclic-diGMP rsw 3Q3Z 2.8 2.7 3.0 A·G SAM rsw 3GX5 2.6 2.5 3.4 A·G SAM + YbxF 3V7E 3.1 3.0 3.3 A·G T-box 4LCK 2.7 2.9 3.2 A·G SAM rsw G2nA 2YGH 2.8 3.3 A·A
N1 class Kt-38 H. m. 1FFK 2.8 2.9 4.7 A·G Kt-7 H. m. (50S) 1FFK 2.7 3.0 4.3 A·G L30e 1T0K 2.7 2.7 4.6 A·G Cobalamine rsw 4GXY 2.5 3.1 5.3 A·G Kt-7 E. c. 2AWB 2.8 3.8 A·G Kt-23 T. t. 2WH1 2.6 A·U Kt-23 T. s. 4AEB 2.5 5.0 A·A
PubMed ID is not available.
Published in 2015
Similarly, A-A pairing is also observed in a ribosome model (PDB code 1FFK) with adenosines in the anti conformation and the N6 amino group in an H-bond with N1 [ 36 ].
Publication Year: 2015
The Biomolecular Interaction Network Database and related tools 2005 update.
(2005) Nucleic Acids Res 33
PubMed: 15608229 | PubMedCentral: PMC540005 | DOI: 10.1093/nar/gki051
BIND's annotation of the intermolecular interfaces between RNA and protein molecules allows a user to select a BIND record with only the interface between two specific molecules within the complex (e.... . BIND ID 109757 from 1FFK, showing the interaction between the large ribosomal subunit rRNA and 50S ribosomal protein L30P from Haloarcula marismortui ).
Publication Year: 2005
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs.
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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