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PDB ID Mentions in PubMed Central Article count: 26

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PDB ID Mentions in PubMed Central

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MeRNA: a database of metal ion binding sites in RNA structures.

(2006) Nucleic Acids Res 34

PubMed: 16381830 | PubMedCentral: PMC1347421 | DOI: 10.1093/nar/gkj058

A. 1976 A32 751 767 Figures and Tables Figure 1 ( a ) Major groove of G-U wobble pair binds a sodium ion (pdb code 1s72); ( b ) AA-platform motif from 23S RNA binds a sodium ion (pdb code 1s72).

Publication Year: 2006

Structural and evolutionary classification of G/U wobble basepairs in the ribosome.

(2006) Nucleic Acids Res 34

PubMed: 16522645 | PubMedCentral: PMC1390688 | DOI: 10.1093/nar/gkl025

The first of these systems, extracted from PDB file 1S72, contains a G/U packed with C/G (P-interaction, abbreviated as GU CG).

(a) and (b) are from PDB file 1S72, ( c ) is from PDB file 1J5E.

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 rRNA 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 ).

Publication Year: 2006

The interaction networks of structured RNAs.

(2006) Nucleic Acids Res 34

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 )

Publication Year: 2006

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities.

(2007) Nucleic Acids Res 35

PubMed: 17567620 | PubMedCentral: PMC1933154 | DOI: 10.1093/nar/gkm334

compute dihedral angles α, β, γ, δ, ε, ζ, χ and pseudorotational phase P for all nucleotides in the 3D structure of 23 S rRNA of Haloarcula mari... mortui with PDB ID 1S72:0.

Publication Year: 2007

The origin and evolution of the ribosome.

(2008) Biol Direct 3

PubMed: 18430223 | PubMedCentral: PMC2386862 | DOI: 10.1186/1745-6150-3-16

The 23S RNA segment, nucleotides 2472 through 2650, (LSU RNA coordinates are from 1S72 .

The equivalent base numbering is given by identifying A2451 with A2486 in reference structure 1S72 .

The RNA segment from 2472–2650 ( 1S72 .

There is apparently a grammatical error in the second sentence which reads "segment from 2427–2462 ( 1S72 .

Also, instead of continually citing structure 1S72 .

Publication Year: 2008

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).

We analyzed the entire reduced-redundancy dataset and, separately, representative 5S, 16S and 23S rRNA structures (PDB files: 1j5e, 2avy, 2j01, 2aw4 and 1s72).

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 file: 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 )].

Publication Year: 2009

A probabilistic model of RNA conformational space.

(2009) PLoS Comput Biol 5

PubMed: 19543381 | PubMedCentral: PMC2691987 | DOI: 10.1371/journal.pcbi.1000406

For the decoy test, we trained the models using the RNA data in the large ribosomal subunit (PDB code 1S72) in order to avoid bias from homologous structures [14] .

Publication Year: 2009

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA.

(2009) Nucleic Acids Res 37

PubMed: 19509311 | PubMedCentral: PMC2724281 | DOI: 10.1093/nar/gkp465

In both PDB ID 1S72 and 1YFV, the GA pairs are also in a sugar-edge/Hoogsteen conformation; however, both pairs in both structures have two base–base hydrogen bonds, a G amino proton to A N7 a... d an A amino proton to G N3 (see Supplementary Figure S3 ).

Hydrogen bonding of this tandem mismatch was investigated in three different PDB structures, the PDB structure (1NKW) of the Deinococcus radiodurans large ribosomal subunit from the Yonath laboratory ( 47 ), the PDB structure (1S72) of the H. marismortui large ribosomal subunit from the Moore and Steitz laboratories ( 48 ) and the PDB structure (1YFV) of a synthetic RNA from the Turner laboratory ( 49 ).

Publication Year: 2009

Classification and energetics of the base-phosphate interactions in RNA.

(2009) Nucleic Acids Res 37

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).

Publication Year: 2009

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

Survey of the simulations Organism Simulated segment Simulation name Resolution (Å); PDB code Simulation length (ns) RMSD (Å) a Ions used in the simulation Escherichia coli 838–... 858, 919–940 E.c. numbering MD_Ec 3.5, 2aw4 b 65 4.3 ± 0.8 41 Na + Deinoccocus radiodurans 851–869, c 933–951 D.r. numbering MD_Dr 3.1, 1nkw 65 5.4 ± 1.0 37 Na + Thermus thermophilus 838–858, 919–940 d E.c. numbering MD_Tt_1 2.8, 2j01 65 5.2 ± 0.9 40 Na + Thermus thermophilus 838–858, 919–940 d E.c. numbering MD_Tt_2 3.8, 1vsp 65 5.0 ± 1.1 40 Na + Haloarcula marismortui 931–952, 1015–1039 H.m. numbering MD_Hm 2.4, 1s72 65 5.4 ± 1.2 45 Na + Haloarcula marismortui 931–952, 1015–1039 H.m. numbering MD_Hm_KCl 2.4, 1s72 65 4.5 ± 1.0 77 K + and 32 Cl − Escherichia coli 838–858, 919–940 E.c. numbering MD_Ec_KCl 3.5, 2aw4 b 30 4.8 ± 0.8 88 K + and 45 Cl − Deinoccocus radiodurans 851–869, c 933–951 D.r. numbering MD_Dr_KCl 3.1, 1nkw 30 3.2 ± 0.9 67 K + and 30 Cl − Thermus thermophilus 838–858, 919–940 d E.c. numbering MD_Tt_1_KCl 2.8, 2j01 30 4.3 ± 1.0 82 K + and 40 Cl − a RMSD values are calculated along the trajectory for the individual snapshots with respect to the starting crystal structure.

Publication Year: 2010

Structural characteristics of novel protein folds.

(2010) PLoS Comput Biol 6

PubMed: 20421995 | PubMedCentral: PMC2858679 | DOI: 10.1371/journal.pcbi.1000750

Structurally equivalent Smotifs between T201 and 1s72 are depicted in the same color-coding.

This is illustrated with Target T0201 (CASP 6) and the S50S ribosomal protein L6P (PDB code 1s72 chain E) that share 3 out of 6 of their Smotifs ( Fig. 8 ).

Three out of the six Smotifs that compose target T0201 are also present in the 50S ribosomal protein L6P (PDB code 1s72 chain E) but in a different topological arrangement.

Publication Year: 2010

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 GC–GC juxtaposition taken from motif L2291 ( E. coli numbering) in the H. marismortui 23S rRNA (pdb entry code 1s72.

( B ) The superposition of the two versions of motif L657 found in the structures of the E. coli (red, pdb entry code 2aw4) ( 16 ) and H. marismortui (green, pdb entry code 1s72) ( 17 ) ribosomes allows the visualization of the local conformational changes in AGPM associated with the GU⇔WC replacement.

( B ) Nucleotide sequence of motif L657 (L657-Hm) from the H. marismortui ribosome (pdb entry code 1s72) ( 17 ).

Publication Year: 2010

Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.

(2010) Nucleic Acids Res 38

PubMed: 20507916 | PubMedCentral: PMC2952862 | DOI: 10.1093/nar/gkq414

( B ) Superposition of the 5S RNA junction from the H. marismortui crystal structure 1S72 ( 91 ) (in tan) and the averaged geometry (in 22–23 ns, in orange) in the 5S_L simulation done over re... idues 16–28 and 57–64 in H2.

Summary of key simulations carried out in this study Name of the simulation Length (ns) Organism (PDB code) Simulated structures (crystal numbering) Ribosomal helices 3WJ nucleotides (crystal numbering) RMSD 3WJ a (Å) Hm_A-site 100 H. marismortui (1JJ2) ( 36 ) 2542–2617 H90–H92 2542–2617 4.4 ± 0.5 Hm_A-site_H90ext b 30 H. marismortui (1JJ2) ( 36 ) 2541–2618 H90–H92 2541–2618 4.6 ± 0.7 Ec_A-site 70 E. coli (2AW4) ( 62 ) 2507–2582 H90–H92 2507–2582 4.5 ± 0.8 Ec_A-site_H90ext b 30 E. coli (2AW4) ( 62 ) 2506–2583 H90–H92 2507–2582 4.3 ± 0.8 Ec_GAC_B 50 E. coli (2AWB) ( 62 ) 1036–1119 H42–H44 1051–1108 1.8 ± 0.2 Ec_GAC_B_nt c 30 E. coli (2AWB) ( 62 ) 1036–1119, 2751 H42–H44 1051–1108 1.6 ± 0.3 Ec_GAC_4 50 E. coli (2AW4) ( 62 ) 1036–1119 H42–H44 1051–1108 1.8 ± 0.2 Ec_GAC_B_ions d 50 E. coli (2AWB) ( 62 ) 1036–1119 H42–H44 1051–1108 1.5 ± 0.2 Hm_GAC 30 H. marismortui (1JJ2) ( 36 ) 1140–1223 H42–H44 1155–1212 2.6 ± 0.3 Hm_GAC_nt c 30 H. marismortui (1JJ2) ( 36 ) 1140–1223, 2786 H42–H44 1155–1212 2.1 ± 0.3 Hm_GAC_3WJ e 50 H. marismortui (1JJ2) ( 36 ) 1155–1212 H42–H44 1155–1212 2.3 ± 0.3 Hm_GAC_parmbsc0 f 50 H. marismortui (1JJ2) ( 36 ) 1140–1223 H42–H44 1155–1212 2.5 ± 0.3 Hm_GAC_anti g 41 H. marismortui (1JJ2) ( 36 ) 1140–1223 H42–H44 1155–1212 2.0 ± 0.3 5S_L h 50 H. marismortui (1S72) ( 91 ) 1–75; 106–120 H1, H2, H3, H5 1–28; 54–75; 106–120 2.4 ± 0.5 5S_S i 50 H. marismortui (1S72) ( 91 ) 4–21; 59–75; 104–119 H1, H2, H5 4–21; 59–75; 104–119 3.2 ± 0.5 Some additional simulations are explained in the text.

Publication Year: 2010

RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.

(2010) Nucleic Acids Res 38

PubMed: 20696653 | PubMedCentral: PMC2952876 | DOI: 10.1093/nar/gkq672

The superimposition of the new E-loop motif found by RNAMoitfScan (red, 1S72, chain `0', 662–669/677–684), a segment of regular A-form helix (green, 1S72, chain `0', 13–20/523&... x02013;530), and a well characterized E-loop motif (blue, 1S72, chain `0', 1639–1646/1539–1546).

( a ) The `kink' regions in kink-turn motifs (red structure: 1QVF, chain `0', 1027–1031; blue structure: 1S72, chain `0', 94–97).

The utility and accuracy of RNAMotifScan is demonstrated by searching for kink-turn, C-loop, sarcin-ricin, reverse kink-turn and E-loop motifs against a 23S rRNA (PDBid: 1S72), which is well characterized for the occurrences of these motifs.

Publication Year: 2010

Non-bulk-like solvent behavior in the ribosome exit tunnel.

(2010) PLoS Comput Biol 6

PubMed: 20975935 | PubMedCentral: PMC2958802 | DOI: 10.1371/journal.pcbi.1000963

Methods Model Setup and Simulation Protocol In order to model solvent dynamics in the ribosome exit tunnel, a cutout from the large ribosomal subunit (pdb code 1S72(2)) was constructed following Petro... e et al [46] .

Publication Year: 2010

Analysis of interactions between ribosomal proteins and RNA structural motifs.

(2010) BMC Bioinformatics 11 Suppl 1

PubMed: 20122215 | PubMedCentral: PMC3009514 | DOI: 10.1186/1471-2105-11-S1-S41

The analysis is conducted on two large ribosomal subunits, HM 50S (PDB no. 1S72) and the 50S subunit of E.coli (EC 50S, PDB no. 2AWB) and on the small subunit of TM 30S (PDB no. 1FJF).

Publication Year: 2010

Gadd45a is an RNA binding protein and is localized in nuclear speckles.

(2011) PLoS One 6

PubMed: 21249130 | PubMedCentral: PMC3017548 | DOI: 10.1371/journal.pone.0014500

Structural data files Apart from the crystal structures used as templates for xtGadd45a homology modelling, the crystal structures of human spliceosomal p15.5 kDa protein bound to a U4 snRNA fragment ... PDB ID 1e7k, [19] ), yeast L30e-mRNA complex (PDB ID 1t0k, [36] ), Haloarcula marismortui ribosomal protein L7Ae-rRNA complex (PDB ID 1s72, [37] ), yeast spliceosomal protein Snu13p dimer complex (PDB ID 1zwz, [38] ) were used.

Publication Year: 2011

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

( b ) The novel GNRA tetraloop instance in 1S72, chain ‘0’, 733-738.

( a ) A known kink-turn instance found in 1S72, chain ‘0’, 1147-1155/1212-1216.

For example, a false prediction made by LENCS in 1S72, chain ‘0’, 2307-2310/2298-2300 contains a trans H/SE U2308-G2299 base pair.

Interestingly, two of the known reverse kink-turn instances (1S72, chain ‘0’ 1527-1529/1662-1664 and 1531-1533/1658-1660) appear to be located close to each other, and manual inspection of the region suggests an instance of tandem reverse kink-turn ( Figure 5 ).

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.

MATERIALS AND METHODS Data preparation The resolved ribosomal RNA subunit structures (1S72 and 1J5E) were downloaded from PDB ( 8 ).

( a ) A known sarcin–ricin instance found in 1S72, chain ‘0’, 1368-1372/2053-2056.

The tandem reverse kink-turn motif instance found in 1S72, chain ‘0’, 1515-1540/1645-1670.

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.

It is worth noting that some known sarcin–ricin motif instances can also be found in the junction loop regions (e.g. the known sarcin–ricin motif instance at 1S72, chain ‘0’, 380-384/405-408).

( A ) A known tandem-sheared instance found in 1S72, chain ‘0’, 2874-2875/2882-2883.

( a ) A known GNRA tetraloop instance in 1S72, chain ‘0’, 252-257.

There are three known reverse kink-turn motif instances in 1S72.

( a ) and ( b ) base pairing pattern of the two hexaloop motif instances identified in CH6: 1S72, chain ‘0’, 1196-1203 and 1S72, chain ‘0’, 1916-1923, respectively.

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’ 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.

Publication Year: 2012

PubMed ID is not available.

Published in 2012

PubMedCentral: PMC3273832

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.

Publication Year: 2012

Comprehensive survey and geometric classification of base triples in RNA structures.

(2012) Nucleic Acids Res 40

PubMed: 22053086 | PubMedCentral: PMC3287178 | DOI: 10.1093/nar/gkr810

( C ) Structure of GCA cWW/Intermediate-HW triple G2580/C2555/A2577 from PDB file 1S72 ( 42 ).

Publication Year: 2012

The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum.

(2012) PLoS One 7

PubMed: 22761677 | PubMedCentral: PMC3382252 | DOI: 10.1371/journal.pone.0038320

( A ) P. falciparum SSU rRNA superimposed on Thermus thermophilus (PDB ID 1J5E; left  =  front/interface side, right  =  back); ( B ) P. falciparum LSU rRNA superimpose... 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.

The P. falciparum LSU rRNA is superimposed on a space-filling model of the three dimensional rRNA structure of Haloarcula marismortui (PDB ID 1S72; left  =  crown/interface side, right  =  back).

Publication Year: 2012

Conformational features of topologically classified RNA secondary structures.

(2012) PLoS One 7

PubMed: 22792195 | PubMedCentral: PMC3390330 | DOI: 10.1371/journal.pone.0039907

A-C were derived from RNA molecule 1S72 ( Haloarcula marismortui) of PDB, and D was derived from 1VC6 ( Hepatitis Delta Virus ).

Publication Year: 2012

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.

Publication Year: 2014

The Nucleic Acid Database: new features and capabilities.

(2014) Nucleic Acids Res 42

PubMed: 24185695 | PubMedCentral: PMC3964972 | DOI: 10.1093/nar/gkt980

For example, the annotation 1S72|1|9|U|99 1S72|1|9|G|83 cWW unambiguously refers to the GU cWW base pair made between two nucleotides in chain 9 of model 1 of PDB file 1S72.

Publication Year: 2014

RNA Bricks--a database of RNA 3D motifs and their interactions.

(2014) Nucleic Acids Res 42

PubMed: 24220091 | PubMedCentral: PMC3965019 | DOI: 10.1093/nar/gkt1084

All occurrences of a sarcin–ricin motif loop, including non-local ones, were found within Haloarcula marismortui 50S ribosomal subunit (PDB: 1S72).

The RNA Bricks web interface displaying details of the H. marismortui large ribosomal subunit (PDB: 1S72).

Publication Year: 2014

The role of nucleobase interactions in RNA structure and dynamics.

(2014) Nucleic Acids Res 42

PubMed: 25355509 | PubMedCentral: PMC4245972 | DOI: 10.1093/nar/gku972

This aspect is illustrated in Figure 1c , that shows the distribution of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{... msbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\bf {r}$\end{document} vectors for all neighboring bases in the crystal structure of the Haloarcula marismortui large ribosomal subunit (PDB code 1S72) ( 2 ) projected on the ρ and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$z$\end{document} coordinates.

Publication Year: 2014