Primary Citation PubMed: 10943889
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In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding.
(2005) Nucleic Acids Res 33
PubMed: 15879350 | PubMedCentral: PMC1090546 | DOI: 10.1093/nar/gki546
Evaluating tRNA tertiary interactions In order to evaluate selected sequences with non-canonical base pairings at sites normally involved in the tertiary fold of tRNA ( 28 ), the selected base pairing... at these positions were examined in the context of the crystal structure of yeast tRNA Phe (PDB entry 1EHZ) ( 29 ).
Publication Year: 2005
Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions.
(2006) Nucleic Acids Res 34
PubMed: 16461956 | PubMedCentral: PMC1361619 | DOI: 10.1093/nar/gkj491
Twenty-one non-redundant structures of free tRNAs (PDB codes: 1ehz, 2tra, 1fir), tRNA-synthetase complexes (PDB codes: 1f7u, 1asz, 1il2, 1c0a, 1o0c, 1n78, 1ffy, 1eiy, 1h4s, 1qf6, 1h3e, 1ser, 1j1u, 1iv... , 1u0b, 1wz2) and tRNA-elongation factor Tu complexes (PDB codes: 1ttt, 1b23) determined by X-ray crystallography at a resolution of 3.3 Å or better were collected from the PDB data archive ( 61 ).
Figure 5 Detail of yeast tRNA Phe X-ray structure at 1.93 Å resolution [PDB code: 1ehz ( 54 )].
This is the yeast tRNA Phe X-ray structure solved at 1.93 Å (PDB code: 1ehz) ( 54 ).
Nevertheless, the N6(A14):N3(A21) H-bond is present in other tRNA structures such as Methanococcus jannaschii tRNA Lys (PDB code: 1j1u) ( 67 ), which also presents the N1(A21):O2′(U8) H-bond as 1ehz, and yeast tRNA Asp (PDB code: 2tra) ( 68 ), which instead presents a N1(A14):O2′(A21) H-bond.
The most represented combination corresponds to that present in the yeast tRNA Phe , which has also the best resolution structure solved to date (Pdb code: 1ehz, resolution 1.93 Å), for seven of the nine interactions.
On these grounds, we chose the structure of tRNA Phe (Pdb code: 1ehz) as the reference system for our calculation of interaction energy of tRNA tertiary base pairing interactions.
L&W 8–14–21 U–A–A 301 (82%) 1ehz 1.93 uracil8…adenine14 Reverse hoogsten (RH) 4 adenine14…adenine21 – – 9–12–23 A–U–A 170 (46%) 1ehz 1.93 uracil12…adenine23 Watson–Crick (WC) 1 adenine9…adenine23 N7-amino,symmetric (N7as) 4 10–25–45 G–C–G 128 (35%) 1ffy 2.10 guanine10…cytosine25 Watson–Crick (WC) 1 guanine10…guanine45 – – m2G-C-G 94 (25%) 1ehz 1.93 N 2 -methylguanine10…cytosine25 Watson–Crick (WC) 1 N 2 -methylguanine10…guanine45 – – 13–22–46 C–G–m7G 179 (49%) 1ehz 1.93 cytosine13…guanine22 Watson–Crick (WC) 1 guanine22…7-methylguanine46 N7-imino (N7i) 4 C–G–G 35 (9%) 1j1u 1.95 C13…G22 Watson–Crick 1 guanine22…guanine46 N7-imino (N7i) 4 15–48 G–C 186 (50%) 1ehz 1.93 guanine15…cytosine48 Reverse Watson–Crick (RWC) 2 18–55 G–Ψ 349 (94%) a 1ehz 1.93 guanine18…pseudouracil55 imino-2-carbonyl, amino-2-carbonyl, bifurcated b 2 G–U 17 (19%) 1j1u 1.95 guanine18…uracil55 c imino:amino-2-carbonyl, bifurcated b 2 19–56 G–C 365 (99%) d 1ehz 1.93 guanine19…cytosine56 Watson–Crick (WC) 1 26–44 m22G–A 94 (25%) 1ehz 1.93 N 2 ,N 2 -dimethylguanine26…adenine44 Imino 1 G–A 46 (12%) 1j1u 1.95 guanine26…adenine44 Imino 1 54–58 T–A 114 (31%) 1c0a 2.40 thymine54…adenine58 Reverse hoogsten (RH) 4 T–m1A 84 (23%) 1ehz 1.93 thymine54…1-methyladenine58 Reverse hoogsten (RH) 4 U–A e 34 (9%) 1j1u 1.95 uracil54…adenine58 Reverse hoogsten (RH) 4 U–m1A e 23 (6%) – – uracil54…1-methyladenine58 Reverse hoogsten (RH) 4 PDB codes of the best resolution structure where each specific interaction is observed are also reported.
Figure 2 Superimposition of the optimized (balls and sticks) and 1ehz X-ray (gray sticks) base triplets.
DISCUSSION Geometries of six out of the nine optimized yeast tRNA Phe tertiary interactions: A9–U12–A23, C13–G22–m7G46, G18–Ψ55, G19–C56, T54–m1A58 and m22G26–A44, reproduce very well those observed in the best resolution structure 1ehz ( Figures 2 and 3 ).
Instead, the A14–A21 interaction is quite weaker in the 1ehz triplet relative to the optimized structure, consequence of the missing A41–A21 H-bond in the X-ray structure.
The rigid body interaction energies of the three possible base pairs in the 1ehz structure are rather similar (within 1.9 kcal/mol) to the interaction energies obtained from the optimized base triplet ( Table 4 ).
Figure 3 Superimposition of the optimized (balls and sticks) and 1ehz X-ray (gray sticks) base pairs.
Publication Year: 2006
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
PubMed: 16600901 | PubMedCentral: PMC1447647 | DOI: 10.1093/nar/gkl116
GRAMM 1.03 ( 32 ) was used to generate 10 000 alternative docking models using the BsTrmB-AdoMet model with the crystal structure of yeast tRNA Phe (Protein Data Bank ID code 1EHZ).
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis.
(2008) Nucleic Acids Res 36
PubMed: 18653533 | PubMedCentral: PMC2528185 | DOI: 10.1093/nar/gkn462
Unique conformation of the anticodon arm of the E. coli initiator tRNA f Met : ( a ) the anticodon arm of tRNA f Met , ( b ) for comparison tRNA Phe anticodon arm (PDB ID 1EHZ), ( c ) the Cm32•... A38 wobble-like base pair observed in crystal structure of tRNA f Met and ( d ) the A37• (G29-C41) base triple observed in crystal structure of tRNA f Met .
Publication Year: 2008
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
(2009) Biol Direct 4
PubMed: 19703275 | PubMedCentral: PMC2749021 | DOI: 10.1186/1745-6150-4-27
Still, in some cases we could find transition metal atoms that interacted directly with nucleotides, namely Zn in the PDB entries 1NLC , 1S03 , 1YXP , 1D9F , Mn in the PDB entries 1EHZ , 1N35 , 1Y3O ,... 2G81 , and so on.
Publication Year: 2009
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.
(2010) Nucleic Acids Res 38
PubMed: 19923230 | PubMedCentral: PMC2817452 | DOI: 10.1093/nar/gkp1010
e thi box gII intron D-loop ac-loop a L-loop hexaloop GNRA loop 15-mer GNRA loop Y-sensor f tri-bulge 1evv 1evv 1evv 1l2x 1q8n 1q9a 1rmn 2cky 2f88 Bases 13–22 30–40 53–61 7... 013;14 14–19 6–22 16–21 26–36 23–27 Best hits RLooM 1ehz* 1mj1 2k4c* 1l3d* 1m90* 2d3o* 3bbn* 3d2x* 1jzx* RMSD a 0.14 0.00 0.15 0.90 0.48 0.16 0.20 0.25 0.44 RMSD b 1.04 0.78 1.11 1.72 4.12 2.76 3.12 0.53 1.58 RMSD s 0.98 0.69 0.90 0.75 2.05 1.05 1.71 0.38 1.34 iFoldRNA RMSD a 1.08 0.30 1.21 0.50 0.48 2.58 0.60 1.39 1.01 RMSD b 10.88 3.90 4.72 4.40 1.26 23.19 2.51 9.21 1.45 RMSD s 6.19 6.42 6.90 5.43 5.31 8.75 5.68 6.31 1.18 Modeled structures are indicated by their PDB identifier and are located in chain A. RMSD a , RMSD between anchors; RMSD b , RMSD between reduced backbones given anchor superposition; RMSD s , structural similarity—RMSD between reduced backbones given optimal superposition, values are given in Å, *: second best template (cf. text).
Publication Year: 2010
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
PubMed: 20139416 | PubMedCentral: PMC2879513 | DOI: 10.1093/nar/gkq031
( A ) The superposition of base pairs G 71 –C 2 (black) and G 4 –U 69 (white) in the structure of the yeast tRNA Phe (pdb entry code 1ehz) ( 40 ).
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.
PubMed: 20507908 | PubMedCentral: PMC2896121 | DOI: 10.1093/nar/gkq483
For the purpose of this comparison, we chose four data sets that contain RNA 3D structures at different scale of length: (i) five tRNAs (1EHZ:A, 1H3E:B, 1I9V:A, 2TRA:A and 1YFG:A) with an average stru... ture length of 76 bp, (ii) three ribozyme P4-P6 domains (1GID:A, 1HR2:A and 1L8V:A) with an average structure length of 157 bp, (iii) two domains V of 23S rRNA (1FFZ:A and 1FG0:A) with an average structure length of 496 bp, and (iv) two 16S rRNAs (1J5E:A and 2AVY:A) with an average structure length of 1522 bp.
The crystal structure of unmodified tRNAPhe from Escherichia coli.
PubMed: 20203084 | PubMedCentral: PMC2896525 | DOI: 10.1093/nar/gkq133
Superposition of unmodified E. coli tRNA Phe (blue) and yeast tRNA Phe in its monoclinic form (yellow, PDB 1EHZ) and orthorhombic form (red, PDB 4TRA).
Phaser ( 43 ) was used to perform a number of searches covering all potential combinations of space groups and search models but the only acceptable solution (RFZ = 4.4 and TFZ = 9.9) was obtained in the space group P 6 2 22 using chain A of yeast tRNA Phe (PDB 1EHZ) ( 7 ).
Stereo view of the structures of unmodified E. coli tRNA Phe (blue) and yeast tRNA Phe in its monoclinic (yellow, PDB 1EHZ) and orthorhombic (red, PDB 4TRA) forms.
The Mg 2+ ion coordinated by U8–A9 and C11–U12 was built octahedrally coordinated by six water molecules and restrained as such during refinement on the basis of the high resolution structures of yeast tRNA Phe (PDB 1EHZ and 1EVV).
( a ) The triplet base pair in the unmodified E. coli tRNA Phe compared with ( b ) the triplet base pair in yeast tRNA Phe (PDB 1EHZ).
Superposition of nucleotides 31–39 of the transcript and mature yeast tRNA Phe (PDB 1EHZ) results in an RMSD of 0.7 Å, illustrating the similarity between the two structures ( Figure 6 b).
RESULTS AND DISCUSSION Crystal structure An unmodified transcript of E. coli tRNA Phe has been crystallized and its structure was determined by molecular replacement using the structure of yeast tRNA Phe (PDB 1EHZ).
Conformational differences between modified and unmodified tRNA In the absence of the crystal structure of modified E. coli tRNA Phe , we compared the present structure with the available structure of the mature yeast tRNA Phe which has been refined at 1.93 Å (monoclinic crystal form, PDB 1EHZ) ( 7 ).
A peak located between the phosphate groups of U8, A9, C11 and U12 was modelled as a Mg 2+ ion coordinated by six water molecules based upon the presence of a similarly coordinated Mg 2+ ion in two high resolution structures of mature yeast tRNA Phe (PDB 1EHZ and 1EVV) ( 7 , 8 ) ( Figure 7 ).
Inspection of aligned structures revealed that while both regions are structurally similar, the relative orientations of the two arms of the tRNA differ between the two structures, with the angle defined by atoms P35, P56, P72 being 73° in the present structure and 67° in mature yeast tRNA Phe in both the monoclinc (PDB 1EHZ) and orthorhombic (PDB 4TRA) crystal forms.
Comparisons of the present structure with yeast tRNA in its monoclinic (PDB 1EHZ) and orthorhombic (PDB 4TRA) crystal forms indicate that the major differences in the loop are the conformations of nucleotides 16 and 17 ( Figure 5 ).
The crystal structure of an 'All Locked' nucleic acid duplex.
PubMed: 20530536 | PubMedCentral: PMC2965234 | DOI: 10.1093/nar/gkq505
Overall geometric helical parameters of selected helices (i) tRNA Phe microhelix, generated from yeast tRNA Phe (1ehz.
Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.
(2011) J Biophys 2011
PubMed: 21716650 | PubMedCentral: PMC3116532 | DOI: 10.1155/2011/219515
Supplementary Table S2 identifies the cryo-EM density maps of each structure and gives the RMSD of each structure relative to the crystal structure of yeast tRNA Phe (PDB code: 1EHZ) [ 33 ].
Both kinked structures for tRNA Phe (PDB code: 1EHZ) and the hybrid state for cryo-EM densities of tRNA are shown.
The A-site structure also resembles the crystal structure of tRNA Phe (1EHZ).
In addition, we computed the RMSDs of the crystal structures, relative to 1EHZ tRNA Phe , and found a range from 0.5 Å to approximately 6 Å (Supplementary Table S1) for superposition of the main stems.
Using Maxwell's demon Molecular Dynamics (MdMD), the starting structure of the native tRNA structures (1EHZ) is driven into conformations that match the cryo-EM data based upon a cross-correlation calculation between a theoretical density for the modeled structure and the experimental cryo-EM density.
Our results confirm that tRNA has a stochastic molecular spring-like motion from the biasing method [ 52 , 54 ], and from the unbiased simulations a nonlinear Brownian type motion from the A/T-structure toward the A-site state model, which matches the free tRNA Phe crystal structure (1EHZ).
Publication Year: 2011
R3D-BLAST: a search tool for similar RNA 3D substructures.
(2011) Nucleic Acids Res 39
PubMed: 21624889 | PubMedCentral: PMC3125779 | DOI: 10.1093/nar/gkr379
For instance, the two tRNAs (PDB IDs: 1EHZ and 3KIX) shown in Figure 1 exhibit similar whole 3D structures, but they have different sequences, lengths and 2D structures annotated in the PDB.
Two tRNAs: ( a ) PDB ID: 1EHZ and chain ID: A; ( b ) PDB ID: 3KIX and chain ID: W; ( c ) superimposition of their 3D structures with Root Mean Square Deviation (RMSD) of 2.457 Å; and ( d ) their 1D sequences (with identity of 44%) and 2D structures annotated in the PDB.
Structural and functional basis for RNA cleavage by Ire1.
(2011) BMC Biol 9
PubMed: 21729333 | PubMedCentral: PMC3149027 | DOI: 10.1186/1741-7007-9-47
(c) Superposition of crystal structures of tRNA Phe (PDB ID 1ehz ) and tRNA Phe from tRNA Phe ·MiaA complex (PDB ID 2zm5 ).
A possible mechanism of stem-loop RNA recognition by Ire1 RNase The crystal structure of tRNA Phe (PDB ID 1ehz ) shows the stem-loop in a conformation that would preclude cleavage by Ire1 (Figure 5c , yellow trace).
MetalionRNA: computational predictor of metal-binding sites in RNA structures.
(2012) Bioinformatics 28
PubMed: 22110243 | PubMedCentral: PMC3259437 | DOI: 10.1093/bioinformatics/btr636
For a tRNA molecule (PDB id: 1EHZ) 76 nt long, with the default number of 7 Mg 2+ hits, it takes ~5 min to obtain the results.
Publication Year: 2012
Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme.
(2012) Nucleic Acids Res 40
PubMed: 21976731 | PubMedCentral: PMC3273808 | DOI: 10.1093/nar/gkr812
The striking structural similarities between the respective sections of the Diels–Alderase ribozyme and tRNA Phe (from yeast, PDB Data set 1EHZ) are highlighted in Figure 7 (for more details, ... ee Supplementary Figure S8 ).
HD-RNAS: An Automated Hierarchical Database of RNA Structures.
(2012) Front Genet 3
PubMed: 22529851 | PubMedCentral: PMC3329738 | DOI: 10.3389/fgene.2012.00059
There are also some PDB entries like 1DFU, 1EHZ etc., where natural sources of the RNA sequences are mentioned in the OTHER_DETAILS field; yet, they have been designated as synthetic ones probably bec... use they have been synthesized by in vitro transcription.
A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders.
(2013) Nucleic Acids Res 41
PubMed: 23580544 | PubMedCentral: PMC3664808 | DOI: 10.1093/nar/gkt219
The resulting model of Stem I is shown in Figure 5 B. Because no tRNA pro structure was available, a tRNA Phe (pdb 1EHZ) is shown instead in Figure 5 B and in the Supplementary pdb Files (Model of Ste... I: Supplementary Data S2 ; tRNA Phe pdb 1EHZ: Supplementary Data S3 ).
A tRNA Phe (pdb 1EHZ) is shown instead of a tRNA Pro (for which no structure is available).
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 1EHZ, base-pairs having MI support in the crystal structure above the specified threshold are colored red, while those in grey are below the threshold.
Small molecule binding, docking, and characterization of the interaction between Pth1 and peptidyl-tRNA.
(2013) Int J Mol Sci 14
PubMed: 24256814 | PubMedCentral: PMC3856088 | DOI: 10.3390/ijms141122741
E. coli Pth1 (PDBID: 2PTH) and tRNA Phe (PDBID:1EHZ) were fit into the mass density.
Modeling results are shown in Figure 2 with atomic coordinates from E. coli Pth1 (PDBID: 2PTH) and tRNA Phe (PDBID: 1EHZ) modeled in.
( a ) After substrate recognition; ( b ) helix 4 clamps the peptide portion (magenta) and CCA terminus of the substrate in the binding channel; ( c ) followed by the enzymatic reaction and release of products or just release of the nucleotide as observed in the SANS model; ( d – e ) Available high and low resolution structures of Pth1 and peptidyl-tRNA on which the model of interaction was built; ( d ) Crystal structures of the complex between Pth1 (PDBID:2PTH, red surface) and the TΨC loop of tRNA (PDBID:3VJR, cyan) with tRNA Phe (PDBID:1EHZ, blue) superimposed; ( e ) SANS model (orange beads) of the interaction presented here with the same coloring as in ( d ); Insets show the orientation of Pth1.
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
Motifs (a–e) from PDBs 1EVV, 1YIJ, 1EHZ, 1FFK and 3CCL, respectively.
All computed interactions are reported with the corresponding PDB code and resolution, of the selected crystal structure Motif Occurrency Interaction PDB; Biomolecule Resolution (Å) Crystallographic 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 ).
Publication Year: 2014
Mechanism of trans-translation revealed by in vitro studies.
(2014) Front Microbiol 5
PubMed: 24600445 | PubMedCentral: PMC3929946 | DOI: 10.3389/fmicb.2014.00065
(A) Saccharomyces cerevisiae tRNA Phe represented by space-filling model (PDB ID: 1EHZ).
Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.
(2014) BMC Res Notes 7
PubMed: 24502340 | PubMedCentral: PMC3930292 | DOI: 10.1186/1756-0500-7-83
Table 1 List of PDB IDs of structures in free-RNA, bound-RNA and DNA dataset Dataset (n) PDB ID free-RNA (88) 157D, 1CSL, 1DQH, 1DUQ, 1EHZ, 1EVV, 1 F27, 1GID, 1HR2, 1I9X, 1KFO, 1KH6, 1L2X, 1LC... , 1MHK, 1NLC, 1NTB, 1NUJ, 1NYI, 1Q29, 1QC0, 1RNA, 1SDR, 1T0D, 1T0E, 1U8D, 1U9S, 1X9C, 1XJR, 1Y26, 1Y27, 1YFG, 1YZD, 1Z79, 1Z7F, 1ZCI, 1ZEV, 1ZFT, 1ZFV, 1ZFX, 1ZX7, 205D, 255D, 280D, 283D, 2A43, 2AO5, 2B57, 2D2K, 2D2L, 2ET5, 2FGP, 2FQN, 2G92, 2H1M, 2OE5, 2OE8, 2OEU, 2OIY, 2PN4, 2PWT, 2Q1O, 2Q1R, 2R20, 2Z75, 353D, 354D, 361D, 364D, 397D, 3B31, 3B4B, 3B5S, 3CJZ, 3CZW, 3D0X, 3D2V, 3DIL, 3DS7, 3FS0, 3FTM, 3GCA, 3GER, 406D, 413D, 420D, 430D, 433D bound-RNA (127) 1A9N, 1B23, 1DFU, 1DI2, 1E7K, 1EC6, 1EFW, 1F7V, 1F7Y, 1FEU, 1G1X, 1GAX, 1H3E, 1H4S, 1I6U, 1IL2, 1J1U, 1JID, 1K8W, 1LNG, 1M5O, 1MJI, 1MZP, 1 N35, 1OOA, 1Q2R, 1QA6, 1QF6, 1QRS, 1QU2, 1R3E, 1R9F, 1RPU, 1S03, 1S72, 1SER, 1TFW, 1U0B, 1URN, 1VFG, 1ZBH, 2ANN, 2AZ2, 2AZX, 2B3J, 2BGG, 2BH2, 2BTE, 2CSX, 2CV1, 2DLC, 2DR8, 2DU3, 2E9T, 2F8K, 2F8S, 2FMT, 2HW8, 2I82, 2NUG, 2NZ4, 2OZB, 2PJP, 2PXV, 2QUX, 2RFK, 2VPL, 2XD0, 2Y8Y, 2ZI0, 2ZJR, 2ZM5, 2ZZM, 3A6P, 3ADD, 3AKZ, 3 AM1, 3AMT, 3AVX, 3BSO, 3CUN, 3DH3, 3EGZ, 3EPH, 3EQT, 3FTF, 3HAX, 3HHN, 3HJW, 3IAB, 3KFU, 3KMQ, 3KS8, 3 L25, 3LRR, 3MOJ, 3MQK, 3NCU, 3NVI, 3OIN, 3OL8, 3OVA, 3QRP, 3R2D, 3R9X, 3RW6, 3SIU, 3SNP, 3TMI, 3TS2, 3UCZ, 3UMY, 3V2F, 3V7E, 3VJR, 4AL5, 4AQ7, 4ATO, 4AY2, 4ERD, 4FVU, 4GCW, 4GD2, 4GHA, 4GHL, 4HXH, 4IG8, DNA (76) 118D, 126D, 137D, 138D, 158D, 160D, 196D, 1D13, 1D23, 1D49, 1D56, 1D57, 1D79, 1D8G, 1 DC0, 1DNZ, 1DOU, 1EHV, 1EN3, 1EN9, 1ENN, 1IKK, 1 M77, 1P4Z, 1S23, 1SGS, 1SK5, 1VJ4, 1WQY, 1XJX, 1XJY, 1ZEX, 1ZEY, 1ZF0, 1ZF1, 1ZF5, 1ZF6, 1ZF7, 1ZF8, 1ZF9, 1ZFA, 1ZFB, 1ZFC, 1ZFF, 1ZFG, 220D, 221D, 240D, 243D, 260D, 2A7E, 2B1B, 2D94, 2D95, 307D, 317D, 348D, 349D, 368D, 369D, 370D, 371D, 395D, 396D, 399D, 414D, 423D, 431D, 441D, 463D, 476D, 477D, 5DNB, 7BNA, 9BNA, 9DNA The number of PDB structures included in each dataset is given within parenthesis.
MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m(2)G and m(2) 2G present in tRNA.
(2013) Comput Struct Biotechnol J 5
PubMed: 24688708 | PubMedCentral: PMC3962230 | DOI: 10.5936/csbj.201302015
Compared with crystal conformer (1EHZ.
This average structure ( Fig. 2B Table 1 ) shows deviations for torsion angle β by 87° and χ by 155° whereas α retains its initial geometry [ 18 ] as found in crystal conformer 1EHZ.
pdb [ 9 ], 1EHZ.
These results are in favor with preferred and alternative conformations of m 2 G obtained by our earlier conformational energy calculations [ 18 ] as well as crystal structure (1EHZ.
RNA Bricks--a database of RNA 3D motifs and their interactions.
PubMed: 24220091 | PubMedCentral: PMC3965019 | DOI: 10.1093/nar/gkt1084
tRNA structure (PDB: 1EHZ) in a reduced graph representation ( D ).
The most conserved part of the T-loop from a high-resolution X-ray structure (PDB: 1EHZ, residues A/53,54,55,56,57,58,61, yellow letters in Figure 3 A) was used to search the RNA Bricks database with default parameters, query-in-motif mode and RNA motifs derived from a non-redundant set of X-ray structures solved at 3.0 Å resolution or better.
PubMed ID is not available.
Published in 2014
A pol III transcript, represented here by tRNA molecule (pdbid: 1EHZ), 15 folded at the distance sufficient for termination, is color coded as in panel A (with loops in pink).
Initial coordinates for modified tRNAs were obtained from the X-ray crystal structures available in the Protein Data Bank: tRNA Asp (PDB code 3TRA, resolution = 3.0 Å), 39 tRNA Phe (PDB code 1... HZ, resolution = 1.93 Å), 40 and tRNA iMet (PDB code 1YFG, resolution = 3.0 Å).
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