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Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments.
(2005) Nucleic Acids Res 33
PubMed: 15860776 | PubMedCentral: PMC1087784 | DOI: 10.1093/nar/gki535
16S 371–376/387–390 1J5E A, B, E Their positions in the molecule is indicated with the PDB number corresponding to the crystal structure and a short description of the structural featu... es.
Publication Year: 2005
NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit.
PubMed: 15939932 | PubMedCentral: PMC1143578 | DOI: 10.1093/nar/gki621
Comparative 3-D modeling of tmRNA.
(2005) BMC Mol Biol 6
PubMed: 15958166 | PubMedCentral: PMC1168896 | DOI: 10.1186/1471-2199-6-14
The 30S ribosomal subunit coordinates (1J5E.
Dependency map of proteins in the small ribosomal subunit.
(2006) PLoS Comput Biol 2
PubMed: 16485038 | PubMedCentral: PMC1364506 | DOI: 10.1371/journal.pcbi.0020010
The atom positions were taken from a T. thermophilus crystal structure obtained for a 3.05 Å resolution [ 13 ] (PDB entry code 1j5e).
Publication Year: 2006
Nucleic acid visualization with UCSF Chimera.
(2006) Nucleic Acids Res 34
PubMed: 16478715 | PubMedCentral: PMC1368656 | DOI: 10.1093/nar/gnj031
Figure 6 The Thermus thermophilus 30S ribosomal subunit ( 7 ) (PDB identifier 1j5e).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
PubMed: 16522645 | PubMedCentral: PMC1390688 | DOI: 10.1093/nar/gkl025
We studied all cis WC G/U basepairs in the 16S rRNA of the bacterium Thermus thermophilus ( Tt )—PDB files 1IBM, 3.31Å resolution, and 1J5E, 3.05Å ( 15 ), and in the 23S/5S rRN... structures of the archaeon Haloarcula marismortui ( Hm )—PDB files 1JJ2 and 1S72, both at 2.4 Å ( 16 ) and the bacterium Deinococcus radiodurans ( Dr )—PDB files 1KPJ and 1LNR, both at 3.10 Å ( 17 ).
(a) and (b) are from PDB file 1S72, ( c ) is from PDB file 1J5E.
Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package.
(2006) BMC Bioinformatics 7
PubMed: 16672074 | PubMedCentral: PMC1513611 | DOI: 10.1186/1471-2105-7-240
The 30S ribosomal subunit structures of Escherichia coli (PDB entry 1M5G) and Thermus thermophilus (PDB entry 1J5E) are retrieved from the protein data bank [ 19 ] and used as template structures for ... he RNA3D program.
The interaction networks of structured RNAs.
PubMed: 17135184 | PubMedCentral: PMC1747187 | DOI: 10.1093/nar/gkl963
Domain B. subtilis 1NBS 3.15 ( 29 ) Full length B.stearothermophilus 2A64 3.30 ( 31 ) 16S rRNA T.thermophilus 1J5E 3.05 ( 35 ) E.coli 2AVY 3.46 ( 36 ) 23S rRNA Transpeptidation site H.marismortui 1S72... 2.40 ( 91 ) TPC + CCA H.marismortui 1Q86 3.00 ( 92 ) TPC E.coli 2AW4 3.46 ( 36 ) Hepatitis delta virus 1DRZ 2.30 ( 40 ) Diels-Alder ribozyme Aptamer 1YLS 3.00 ( 37 ) Hairpin ribozyme Viroïd RNA 1HP6 2.40 ( 44 ) Hammerhead ribozyme All RNA 1MME 3.10 ( 48 ) Whole S.mansoni 2G0Z 2.20 ( 49 ) Guanine riboswitch With hypoxanthine B.subtilis 1U8D 1.95 ( 51 ) With guanine 1Y27 2.40 ( 50 ) With adenine 1Y26 2.10 ( 50 ) TPP riboswitch E.coli 2GDI 2.05 ( 54 ) SAM riboswitch T.tengcongensis 2GIS 2.90 ( 52 )
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction.
PubMed: 17130160 | PubMedCentral: PMC1761430 | DOI: 10.1093/nar/gkl819
In the 30S ribosomal proteins, we omitted the THX subunit (chain V in 1J5E) and in the 50S ribosomal proteins, we omitted the L10 (chain G in 1JJ2) and L39E (chain 1) subunits.
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
(2008) Nucleic Acids Res 36
PubMed: 18346970 | PubMedCentral: PMC2377432 | DOI: 10.1093/nar/gkn112
Structure of the bacterial A site in the ‘off’ state A stereoview with the secondary structure of the bacterial A site in the ‘off’ state found in the BACT-Co crystal i... shown in Figure 3 a. Its conformation is similar to the bacterial ‘off’ state found in the T. thermophilus 30S ribosomal particle with a root mean square deviation (RMSD) of 1.1 Å [PDB ID: 1J5E in ( 3 )].
Two A sites in the duplex have almost identical conformations except for the A1492 residue ( Supplementary Figure 9a ), and are similar to the bacterial ‘off’ state with tucked-in A1492 and A1493 found in the Thermus thermophilus 30S ribosomal particle [PDB ID: 1J5E in ( 3 )].
Publication Year: 2008
Revealing unique properties of the ribosome using a network based analysis.
PubMed: 18625614 | PubMedCentral: PMC2504294 | DOI: 10.1093/nar/gkn433
Similarly, we compared between the T. thermophilus (PDB code 1J5E) 16S rRNA network ( Table 1 ) and the 30S structure that comprises the 16S rRNA and the ribosomal proteins (3850 edges and 18 929 edge... ).
To study the properties of the ribosome network, we investigated the topological properties of four rRNA networks, including the small ribosomal subunit (PDB code 1J5E), two large ribosomal subunits (PDB codes 1NKW, 1JJ2) and the rRNA of the entire ribosome structure (PDB codes 2AVY, 2AW4).
Frequency and isostericity of RNA base pairs.
(2009) Nucleic Acids Res 37
PubMed: 19240142 | PubMedCentral: PMC2673412 | DOI: 10.1093/nar/gkp011
Fraction of nucleotides in the 5S, 16S and 23S rRNA 3D structures of E. coli (PDB files: 2aw4 and 2avy) and T. thermophilus (PDB files: 2j01 and 1j5e) and the 5S and 23S rRNAs of H. marismortui (PDB f... le: 1s72) that form cWW and non-cWW base pairs, base-stacking and base–phosphate interactions Bases forming base pairs cWW base pairs and no non-cWW base pair 52% cWW base pairs and at least one non-cWW base pairs 7% At least one non-cWW base pairs and no cWW base pairs 20% Bases forming other interactions (no base pairing) Base-stacking and base–phosphate interaction 13% Base–stacking only 3% Base–phosphate only 1% Bases forming no RNA–RNA interactions 4% Total 100% Base pair exemplars and online base pair catalog To compare base pairs between and within geometric families, we have identified a single representative, called the exemplar , for each base combination (i.e. AA, AC, AG, …, UU) that makes a pair in a given geometric family as described in the ‘Materials and methods’ section.
The second set of four numbers in each row reports the results obtained only using base pairs drawn from five representative rRNA structures [50S H. marismortui (PDB: 1s72), E. coli (PDB: 2aw4) and T. thermophilus (PDB: 2j01) and 30S E. coli (PDB: 2avy) and T. thermophilus (PDB: 1j5e)].
3D structural alignments were constructed for the rRNAs of E. coli, T. thermophilus and H. marismortui , using the PDB files 2awb and 2aw4 ( E. coli ), 2j01, 2j03 and 1vsa ( T. thermophilus ) and 1s72 ( H. marismortui ) for 5S and 23S rRNAs and PDB files 2aw7 and 2avy ( E. coli ) and 1j5e, 2j00, 2j02 and 2ow8 ( T. thermophilus ) for 16S rRNAs.
Construction of rRNA 3D structural alignments The FR3D program suite was used to extract base pairs from the selected 3D files of the 5S, 16S and 23S rRNAs of E. coli [PDBs: 2avy, 2aw7, 2aw4 and 2awb ( 10 )], T. thermophilus [PDBs: 1j5e ( 11 ), 2j00, 2j01, 2j02 and 2j03 ( 12 ), 2ow8 and 1vsa ( 13 )] and H. marismortui [PDB: 1s72 ( 14 )].
We analyzed the entire reduced-redundancy dataset and, separately, representative 5S, 16S and 23S rRNA structures (PDB files: 1j5e, 2avy, 2j01, 2aw4 and 1s72).
Base pair counts and percent frequencies for the tWH base pair family, with simultaneous 95% CIs Each cell contains data from four sources: (1) pink: 5S, 16S and 23S bacterial sequence alignments; (2) orange: 5S, 16S and 23S E. coli ribosome 3D structure (2avy and 2aw4); (3) yellow: 5S, 16S and 23S T. thermophilus ribosome structure [1j5e and 2j01( 11 , 12 )]; and (4) cyan: reduced-redundancy dataset of PDB files.
Publication Year: 2009
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA.
PubMed: 19509311 | PubMedCentral: PMC2724281 | DOI: 10.1093/nar/gkp465
The PDB structure (1J5E) of the Thermus thermophilus 30S ribosomal subunit from the Ramakrishnan laboratory ( 46 ) revealed that both G•A pairs are forming sugar-edge/Hoogsteen pairs.
Classification and energetics of the base-phosphate interactions in RNA.
PubMed: 19528080 | PubMedCentral: PMC2731888 | DOI: 10.1093/nar/gkp468
Construction of rRNA 3D structural alignments The FR3D program suite, modified as described above was used to identify and classify BPh interactions from selected 3D files of the 16S and 23S rRNAs of ... . coli— PDBs: 2avy and 2aw4 ( 39 )—and T. thermophilus— PDBs: 1j5e ( 40 ) and 2j01 ( 41 ).
Frequencies of non-self BPh interactions in E. coli and T. thermophilus 16S and 23S rRNAs 16S rRNA 3D structures 23 S rRNA 3D structures Escherichia coli (2avy) (1j5e) Thermus thermophilus (lj5e) Escherichia coli (2aw4) Thermus thermophilus (2j01) Total nucleotides 1530 1513 2841 2772 Number of distinct bases involved in BPh interactions 185 (12.1%) 191 (12.6%) 372 (13.1%) 371 (13.4%) Total number of BPh interactions 195 203 397 398 Number of BPh interactions at corresponding E. coli and T. thermophilus positions 174 338 Conserved bases at corresponding BPh positions About 13% of all bases in the bacterial rRNA structure from BPh interactions and ∼86% of these interactions are common to the E. coli and T. thermophilus rRNA structures.
Conservation of BPh interactions between homologous RNA 3D structures Using FR3D, we extracted, classified and aligned all BPh interactions for the 16S and 23S rRNA structures of E. coli (2avy and 2aw4) and T. thermophilus (1j5e and 2j01), as described in the ‘Materials and Methods’ section.
Ion-induced folding of a kink turn that departs from the conventional sequence.
PubMed: 19783814 | PubMedCentral: PMC2790904 | DOI: 10.1093/nar/gkp791
Comparison of C1′–C1′ distances for the base pairs of the NC helix in Kt-23 of T. thermophilus ( T. th ) and E. coli ( E. co ), Kt-7 and the U4 snRNA k-turn Kt-23 ( T. th ) Kt-... 3 ( E. co ) Kt-7 U4 1b•1n G•A 9.3 Å G•A 9.3 Å G•A 9.2 Å G•A 9.6 Å 2b•2n A•U 9.9 Å A•U 9.6 Å A•G 9.4 Å A•G 9.0 Å 3b•3n U•G 11.0 Å G•G 11.4 Å A•G 10.0 Å G–C 10.8 Å 4b•4n A•A 12.3 Å A–U 10.8 Å G-C 10.4 Å G–C 10.9 Å These were measured from the PDB coordinate files 1J5E (Kt-23, T. th ) ( 22 ), 2AVY (Kt-23, E .
All images of the Kt-23 structure were made using PDB file 1J5E ( 22 ).
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
(2010) Nucleic Acids Res 38
PubMed: 20139416 | PubMedCentral: PMC2879513 | DOI: 10.1093/nar/gkq031
( B ) The GU-like juxtaposition observed in base pairs A 105 –C 112 and A 113 –C 104 (pdb entry code 402d) ( 27 ), A 11 –C 22 and A 27 –C 6 (pdb entry code 405d) ( 28 )... A 5 –C 24 and A 23 –C 6 (pdb entry code 1d4r) ( 29 ), A 139 –C 158 and A 157 –C 140 (pdb entry code 1jid) ( 30 ), A 26 –C 44 (pdb entry codes 1o0b, 1qtq, 1gtr, 1qru) ( 31–34 ), A 1500 –C 1402 (pdb entry code 1j5e) ( 35 ), A 192 –C 178 (pdb entry code 1u9s) ( 36 ) and A 44 –C 26 (pdb entry code 1y27) ( 37 ).
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 .
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.
PubMed: 20507908 | PubMedCentral: PMC2896121 | DOI: 10.1093/nar/gkq483
Superposition display of iPARTS global alignment between two 16S rRNA 3D structures of T. thermophilus (PDB ID: 1J5E, chain ID: A, length: 1513 bp) colored green and E. coli (PDB ID: 2AVY, chain ID: A... length: 1530 bp) colored orange with an RMSD of 7.491 Å.
Finally, we tested iPARTS on two 16S rRNA 3D structures of Thermus thermophilus (PDB ID: 1J5E; NDB ID: RR0052, chain ID: A, length: 1513 bp) and Escherichia coli (PDB ID: 2AVY; NDB ID: RR0123, chain ID: A, length: 1530 bp) to demonstrate its capability for aligning large RNAs, which still remains a challenge to date due to their large size.
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 structure 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.
A model for the study of ligand binding to the ribosomal RNA helix h44.
PubMed: 20215440 | PubMedCentral: PMC2910043 | DOI: 10.1093/nar/gkq159
Stereo view of a superposition of the hygromycin B binding site in HX RNA (white backbone) and the corresponding region in the crystal structures of the ribosomal 30S subunit, free (orange, PDB 1J5E; ... MSD = 1.2 Å) ( 25 ) and in complex with the aminoglycoside ligand (green, PDB 1HNZ; RMSD = 1.1 Å) ( 7 ).
RMSD values were calculated for superposition of residues C1403–C1409 and G1494–U1498; RMSD of 1J5E versus 1HNZ=0.4 Å.
Structural signatures of antibiotic binding sites on the ribosome.
PubMed: 20494981 | PubMedCentral: PMC2952860 | DOI: 10.1093/nar/gkq411
The interface with ribosomal proteins was calculated on the PDB IDs 1JJ2 and 1J5E.
Having applied the procedure to the apo-structures of the T. thermophilus small ribosomal subunit (PDB ID 1J5E) and the H. marismortui large subunit (PDB ID 1JJ2), we extracted a total of 17 610 overlapping pockets that differ in at least 1 nt ( Supplementary Table S4 ).
Furthermore, the atoms of the binding sites were defined in the apo structures of the small ribosomal subunit of T. thermophilus (PDB 1J5E) ( 18 ) and E. coli (PDB 2AVY) ( 19 ), and the large ribosomal subunit of H. marismortui (PDB 1JJ2) ( 20 ) and D. radiodurans (PDB 2ZJR) ( 21 ).
The program was applied to the PDB IDs 1J5E, 2AVY, 1JJ2 and 2ZJR files, excluding ions and including all ATOM coordinates (rRNA and ribosomal proteins).
The pocket was calculated on the crystal structure of T. thermophilus (PDB ID 1J5E) and was superimposed to the bound structure (PDB ID 1HNW).
Finally, we retained only pockets that comprise 12 nt and differ in at least 1 nt, resulting in 17 610 (calculated for PDB 1J5E and 1JJ2) pockets that we refer to as the background.
Centrality measures We modeled the 16S rRNA (PDB IDs 1J5E, 2AVY) and the 23S rRNA (PDB IDs 1JJ2, 2ZJR) as a structure-based network of interacting nts ( 31 ).
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.
PubMed: 20696653 | PubMedCentral: PMC2952876 | DOI: 10.1093/nar/gkq672
To demonstrate this, we selected three PDB entries with different resolutions for the same 16S rRNA structure from Thermus thermophilus (PDBid: 2VQE, 1J5E and 1I95), and used RNAMotifScan to identify ... he five motifs in them.
bp #KT #CL #SR #RK #EL 2VQE 2.50 Å 1522 766 433 333 3 0 2 0 6 1J5E 3.05 Å 1522 761 434 327 2 0 2 0 6 1I95 4.50 Å 1514 699 422 277 1 0 0 0 3 The columns in the tables represent PDB codes of the RNA structures, the resolution, the length, the number of base pairs (bp) annotated by MC-Annotate, the number of annotated canonical base pairs (Can.
Geometric properties of nucleic acids with potential for autobuilding.
(2011) Acta Crystallogr A 67
PubMed: 21173468 | PubMedCentral: PMC3006036 | DOI: 10.1107/S0108767310039140
Even for the ribosome structure (PDB code 1J5E, using experimental amplitudes and phases to 3.05 Å resolution and masking out the protein), 1455 out of 1513 phosphates (96%) are correc... ly found with an overall r.n. = 4.4 (details not shown).
The algorithms work rather well for phosphates even for experimental phases of complicated structures like the ribosome (PDB code 1J5E) at 3.05 Å resolution.
1J5E is the PDB code of the 30S ribosomal subunit determined at 3.05 Å resolution and shown for comparison with the RNA histograms.
Publication Year: 2011
ModeRNA: a tool for comparative modeling of RNA 3D structure.
(2011) Nucleic Acids Res 39
PubMed: 21300639 | PubMedCentral: PMC3105415 | DOI: 10.1093/nar/gkq1320
The model of T. thermophilus 23S rRNA based on the 2AVY structure, and the model of the E. coli 23S rRNA based on the 1J5E structure exhibited an all-atom RMSD of 5.5 and 5.2 Å, respec... ively.
Two more complicated example models were built for 23S rRNA sequences extracted from the 30S ribosomal subunit structures of T. thermophilus (1J5E) and E. coli (2AVY) using each other as templates.
Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.
(2012) Nucleic Acids Res 40
PubMed: 21976732 | PubMedCentral: PMC3273805 | DOI: 10.1093/nar/gkr804
We applied our new clustering framework on two data sets (one for hairpin loop instances and the other for internal loop, bulge loop and junction loop instances, see ‘Materials and Methods... 019; section) that contain 5S ( Haloarcula marismortui , PDBid: 1S72, chain ‘9’), 16S ( Thermus thermophilus , PDBid: 1J5E, chain A) and 23S ( Haloarcula marismortui , PDBid: 1S72, chain ‘0’) ribosomal RNAs.
For example, the GNRA tetraloop instance 1S72, chain ‘0’, 1326-1331 was missed due to the fact that the G1327-A1330 sheared pair is replaced by trans W/H pair, while the instances 1S72, chain ‘0’, 1706-1712 and 1J5E, chain A, 691-696 were missed because the closing canonical pair is replaced by sheared pairs.
( b ) The potential novel kink-turn instance found in 1J5E, chain A, 242-247/277-284.
MATERIALS AND METHODS Data preparation The resolved ribosomal RNA subunit structures (1S72 and 1J5E) were downloaded from PDB ( 8 ).
( a ) A novel kink-turn instance found in 1J5E, chain A, 515-521/528-536.
The LENCS method has also successfully identified all four instances, but include three other unrelated motif instances, where one of them appears to be a sarcin–ricin motif instance (1J5E, chain A, 446-450/483-488) and the other two are kink-turn motif instances (1S72, chain ‘0’, 241-244/267-270 and 1J5E, chain A, 683-687/703-707).
Three novel sarcin–ricin instances: ( b ) 1J5E, chain A, 483-487/447-450, ( c ) 1S72, chain ‘0’, 1971-1974/2009-2010 and ( d ) 1S72, chain ‘0’, 1251-1254/911-912.
FR3D identified 21 GNRA tetraloop motif instances from 1S72 23S rRNA and 12 from 1J5E 16S rRNA.
Publication Year: 2012
PubMed ID is not available.
Published in 2012
This motif is found in both 23S (PDBid: 1S72, chain ‘0’, 1254-1255/1101-1108) and 16S rRNA (PDBid: 1J5E, chain A, 880-881/569-575), indicating their potential structural or functional ... mportance.
A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.
(2012) PLoS Comput Biol 8
PubMed: 22654657 | PubMedCentral: PMC3359968 | DOI: 10.1371/journal.pcbi.1002530
Methods Analysis of contacts in the assembled 30S subunits In the current study, we analyze the crystal structures of the 30S subunits from the Escherichia coli (PDB  ID 2AVY  ) and Thermus the... mophilus ribosomes (PDB ID 1J5E  ).
The starting conformations of r-proteins for the MD were obtained from the crystal structures of the 30S subunits ( E. coli 2AVY and T. thermophilus 1J5E).
Structural constraints identified with covariation analysis in ribosomal RNA.
(2012) PLoS One 7
PubMed: 22724009 | PubMedCentral: PMC3378556 | DOI: 10.1371/journal.pone.0039383
For all neighbor effects, the atomic level physical distance between the atoms are estimated from the three-dimensional high-resolution crystal structure (16S rRNA:,PDBID 1J5E; 5S and 23S rRNA: PDBID ... AW4).
The high-resolution crystal structure of the T. thermophilus 30S ribosomal subunit (PDBID: 1J5E) which contains the 16S rRNA and E. Coli 50S ribosomal subunit (PDBID: 2AW4)are the reference structures for this study.
The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum.
PubMed: 22761677 | PubMedCentral: PMC3382252 | DOI: 10.1371/journal.pone.0038320
The P. falciparum mt SSU rRNAs are superimposed on a space-filling model of the three dimensional rRNA structure of Thermus thermophilus (PDB ID 1J5E; left = front/interface side, ri... ht = back).
( A ) P. falciparum SSU rRNA superimposed on Thermus thermophilus (PDB ID 1J5E; left = front/interface side, right = back); ( B ) P. falciparum LSU rRNA superimposed on Haloarcula marismortui (PDB ID 1S72; left = crown/interface side, right = back); ( C–E ) secondary structure diagrams for SSU, 5′ LSU, and 3′ LSU rRNAs, respectively, with each P. falciparum mt rRNA fragment color-coordinated with the fragment colors in the three-dimensional structure.
Structure based hypothesis of a mitochondrial ribosome rescue mechanism.
(2012) Biol Direct 7
PubMed: 22569235 | PubMedCentral: PMC3418547 | DOI: 10.1186/1745-6150-7-14
The conformation of the universally conserved ribosome decoding site nucleotides A-1492 and A-1493 is shown (C) in case of an empty A-site with both bases stacked (from PDB entry 1J5E [ 11 ]), (D) wit... mRNA and a cognate tRNA present in the A-site and both bases unstacked (from PDB entry 1IBM [ 12 ]) and (E) with a stop codon and a release factor present in the A-site in an intermediate state (from PDB entry 3MR8 [ 8 ]).
A structural basis for streptomycin-induced misreading of the genetic code.
(2013) Nat Commun 4
PubMed: 23322043 | PubMedCentral: PMC3552334 | DOI: 10.1038/ncomms2346
The root-mean-square deviation (rmsd) between all 16S rRNA phosphate atoms of our apo 30S structure and the equivalent PDB entry 1J5E 12 is 0.79 Å, and the rmsd between our MAP structure and P... B entry 1IBL 9 is 0.48 Å ( Supplementary Fig.
In comparison, the rmsds between open and closed 30S structures are 1.2 Å between the Apo and MAP data sets and 0.97 Å between the analogous PDB entries 1J5E and 1IBL 9 , 12 , 13 .
Coordinates of the 30S subunit structure (PDB accession code 1J5E 12 ) with additional RNA and protein modifications were used for initial rigid body refinement with Phenix 14 for the Apo, Strep, and Par data sets (PDB accession code 2VQE 44 ) was used for all other data sets).
Publication Year: 2013
MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(?) only models, Alternative alignments, and Non-sequential alignments.
(2013) BMC Bioinformatics 14
PubMed: 23331634 | PubMedCentral: PMC3637537 | DOI: 10.1186/1471-2105-14-24
One of the most interesting examples of such protein pairs is that of KH domains of hnRNP K (PDB entry 1KHM) and ribosomal protein S3 (PDB entry 1J5E) [ 11 ].
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
(2013) Nucleic Acids Res 41
PubMed: 24005040 | PubMedCentral: PMC3905863 | DOI: 10.1093/nar/gkt795
For example, the pipeline is able to model all base pairs of C-loop C15 with PDBid 1J5E ( 44 ).
The 16S rRNA of T hermus thermophilus contains in an internal loop of helix 17 a sarcin-ricin motif at position 446–450/484–488 based on the annotation in ( 45 ) (PDBid 1J5E).
Another tandem GA/AG instance is located in the 16S rRNA (PDBid 1J5E) at sequence position 1394–1397/1454–1457.
A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly.
(2013) BMC Biophys 6
PubMed: 24152303 | PubMedCentral: PMC4016315 | DOI: 10.1186/2046-1682-6-13
In our previous work, we used the X-ray crystal structures of 30S for two bacterial species, E. coli [PDB: 2AVY] [ 41 ] and T. thermophilus [PDB: 1J5E] [ 42 ], to identify contact residues as amino ac... ds containing at least one atom within 3.5Å of any nucleic acid atom.
Determination of ribosomal protein-RNA contact sites and protein net charge The r-protein/rRNA contact sites were obtained from the E. coli [ 41 ] [PDB: 2AVY] and T. thermophilus [ 42 ] [PDB: 1J5E] 30S x-ray crystal structures, accessed from the Protein Data Bank [ 45 ].
Structural basis for the interaction of protein S1 with the Escherichia coli ribosome.
(2015) Nucleic Acids Res 43
PubMed: 25510494 | PubMedCentral: PMC4288201 | DOI: 10.1093/nar/gku1314
Crystal structures of 30S subunits from T. thermophilus (pdb accession code: 1j5e ( 44 )) and E. coli (pdb accession code: 3ofo ( 40 )) were filtered to comparable resolutions using the Molmap functio... in Chimera.
Difference electron density maps were then calculated in SPIDER ( 37 ) by subtracting the filtered map for T. thermophilus 30S subunit (pdb accession code: 1j5e ( 44 )) or E. coli 30S subunit (pdb accession code: 3ofo ( 40 )) from either EMD-1003 ( 45 ) or the ErmCL–SRC map (Supplementary Figure S4A–D).
Publication Year: 2015
The structure of a rigorously conserved RNA element within the SARS virus genome.
(2005) PLoS Biol 3
PubMed: 15630477 | PubMedCentral: PMC539059 | DOI: 10.1371/journal.pbio.0030005
The RCSB Protein Data Bank accession numbers for the other protein and RNA structures discussed in this paper are as follows: the 30S ribosome (1J5E), the 30S ribosome in which prokaryotic IF-1 has be... n added (1HR0), the eukaryotic analog of prokaryotic IF-1 (1D7Q), and the crystal structure of nsp9 (1QZ8 and 1UW7).
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