Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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LocalMove: computing on-lattice fits for biopolymers.

(2008) Nucleic Acids Res 36

PubMed: 18556754 | PubMedCentral: PMC2447748 | DOI: 10.1093/nar/gkn367

FCC lattice fits for the full backbone of two ribozymes models [PDB IDs 1SJ3:R (left panel) and 1GID:A (right panel)] superimposed with their original models.

Publication Year: 2008


Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads.

(2009) Nucleic Acids Res 37

PubMed: 19043070 | PubMedCentral: PMC2632901 | DOI: 10.1093/nar/gkn918

CChMVd (+) full-length hammerhead model building After superimposing NMR structures of CChMVd domains I− and II+ on domains I and II of the crystal structure of the Schistosoma hammerhead ( 12... ), we removed the crystallographic domain I and II atoms and inserted the unpaired A11 nucleotide at the base of stem II ( Figure 1 A) in a stacked conformation, using PDB structure 1GID ( 24 ) as a model.

Publication Year: 2009


BPS: a database of RNA base-pair structures.

(2009) Nucleic Acids Res 37

PubMed: 18845572 | PubMedCentral: PMC2686499 | DOI: 10.1093/nar/gkn676

Figure 4 illustrates representative search results obtained for a given structure ID, here the ID of the P4-P6 group I ribozyme domain ( 14 ): URX053 (NDB_ID); 1GID (PDB_ID).

Publication Year: 2009


Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.

(2009) Bioinformatics 25

PubMed: 19812110 | PubMedCentral: PMC2788923 | DOI: 10.1093/bioinformatics/btp576

P4-P6 RNA ribozyme domain (‘P4-P6’, PDB ID 1GID) 158 residues (Cate et al .

RMSD of minimized full atomic structures Molecule Overall Helical Non-helical ID RMSD (Å) fragments fragments RMSD (Å) RMSD (Å) Validation structures (10 models) 1KXK 2.13 ± 0.21 1.36 ± 0.44 2.41 ± 1.39 6TNA 2.81 ± 0.11 1.10 ± 0.09 3.02 ± 1.27 3CUL 3.06 ± 0.18 1.77 ± 0.82 2.48 ± 1.90 1GID 3.16 ± 0.08 2.03 ± 1.22 2.75 ± 1.45 1ZZN 2.79 ± 0.16 2.10 ± 0.74 2.56 ± 1.42 1Y0Q 2.76 ± 0.07 1.92 ± 0.68 2.50 ± 1.54 NAST tRNA models (50 models) Model A 8.39 ± 0.27 2.65 ± 0.71 4.13 ± 1.91 Model B 13.30 ± 0.31 3.08 ± 1.28 3.82 ± 1.51 Model C 15.99 ± 0.76 3.06 ± 1.13 4.19 ± 1.95 We report both overall RMSD values and separate values for helical and non-helical fragments.

Evaluation of minimized full atomic structures with MolProbity and the RCSB ADIT tool Molecule ID MolProbity RCSB ADIT Clashscore (goal=0) Percentile ( N =1784) Covalent bonds Covalent angles Crystal structure Best model Average (10 models) Crystal structure Best model Average (10 models) RMSD (Å) RMSD (degrees) Crystal Models Crystal Models 1KXK 14.03 3.33 8.54 ± 5.54 54 97 78.30 ± 22.53 0.006 0.017 0.9 2.8 6TNA 26.46 4.92 9.11 ± 4.54 19 94 76.60 ± 19.10 0.079 0.017 3.4 2.7 3CUL 7.67 6.11 8.56 ± 2.30 83 90 79.10 ± 10.81 0.007 0.020 1.0 3.2 1GID 35.78 13.31 23.21 ± 14.67 10 57 35.80 ± 18.36 0.009 0.031 0.9 3.4 1ZZN 32.67 15.29 29.46 ± 9.82 13 48 21.11 ± 16.00 0.008 0.032 1.1 3.6 1Y0Q 40.47 15.9 40.82 ± 17.72 8 46 13.60 ± 15.03 0.007 0.036 1.0 3.8 We give MolProbity Clashscores and percentiles for validation structures.

Publication Year: 2009


iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.

(2010) Nucleic Acids Res 38

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.

Publication Year: 2010


HD-RNAS: An Automated Hierarchical Database of RNA Structures.

(2012) Front Genet 3

PubMed: 22529851 | PubMedCentral: PMC3329738 | DOI: 10.3389/fgene.2012.00059

PDB Chain BLAST result PDB description 1ASY R, S BLAST gb M25168.1 YSCTRDCER S.cerevisiae Asp-tRNA 149 2e-34 Yeast aspartyl-tRNA synthetase complexed with tRNA Asp 1ASZ R, S BLAST gb M25168.1 YSCTRDCE... S.cerevisiae Asp-tRNA 149 2e-34 Yeast aspartyl-tRNA synthetase complexed with tRNA Asp 1GID A, B BLAST emb V01416.1 Fragments of a Tetrahymena gene for 26s rRNA with… 311 8e-83 Tetrahymena group I INTRON 1HR2 A, B BLAST emb V01416.1 Fragments of a Tetrahymena gene for 26s rRNA with… 295 4e-78 Tetrahymena group I INTRON 1IVS C, D BLAST dbj AB080139.1 Thermus thermophilus tRNA-Val 149 2e-34 Thermus thermophilus valyl-tRNA synthetase complexed with tRNA(VAL) 1U9S A BLAST gb AE017221.1 Thermus thermophilus HB27, complete genome 319 3e-85 Thermus thermophilus 1VTQ A BLAST gb M25168.1 YSCTRDCER S.cerevisiae Asp-tRNA 149 2e-34 Yeast t-RNA-Asp 2CSX C, D BLAST gb AE000657.1 Aquifex aeolicus VF5, complete genome 149 2e-34 Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(MET) 2CT8 C, D BLAST gb AE000657.1 Aquifex aeolicus VF5, complete genome 147 1e-33 Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(MET) 2CV0 C, D BLAST gb AE017221.1 Thermus thermophilus HB27, complete genome 149 2e-34 Glutamyl-tRNA synthetase from thermus thermophilus in complex with tRNA(GLU) 2CV1 C, D BLAST gb AE017221.1 Thermus thermophilus HB27, complete genome 149 2e-34 Glutamyl-tRNA synthetase from thermus thermophilus in complex with tRNA(GLU) 2CV2 C, D BLAST gb AE017221.1 Thermus thermophilus HB27, complete genome 149 2e-34 Glutamyl-tRNA synthetase from thermus thermophilus in complex with tRNA(GLU) 2DXI C, D BLAST gb AE017221.1 Thermus thermophilus HB27, complete genome 149 2e-34 Glutamyl-tRNA synthetase from thermus thermophilus complexed with tRNA(GLU) 2IHX B BLAST gb M21526.1 ALRSRCAC Rous sarcoma virus defective mutant PR2257… 149 2e-34 Sequence occurs naturally in rous sarcoma virus (RSV) 2NOQ A BLAST gb AF218039.1 AF218039 Cricket paralysis virus non-structural pol… 377 e-102 Ribosome-bound cricket paralysis virus IRES RNA 2ZNI C, D BLAST dbj AP008230.1 Desulfitobacterium hafniense Y51 DNA, complete g… 143 1e-32 Pyrrolysyl-tRNA synthetase-tRNA(PYL) complex from desulfitobacterium hafniense 3AKZ F, H, G, E BLAST gb AE000512.1 Thermotoga maritima MSB8, complete genome 147 1e-33 Thermotoga maritima non-discriminating glutamyl-tRNA synthetase in complex with tRNAGLN 3AL0 E BLAST gb AE000512.1 Thermotoga maritima MSB8, complete genome 147 1e-33 Glutamine transamidosome from thermotoga maritima in the glutamylation state 3FOZ D BLAST gb CP002185.1 Escherichia coli W, complete genome 137 3e-3137 8e-31 E. Coli isopentenyl-tRNA transferase in complex with E. coli tRNA(PHE) 3Q50 A BLAST gb AE008691.1 Thermoanaerobacter tengcongensis MB4, complete ge… 66 8e-10 Based on the sequence of class I, type 1 PREQ1 riboswitch aptamer from T. tengcongensis 3Q51 A BLAST gb AE008691.1 Thermoanaerobacter tengcongensis MB4, complete ge… 66 8e-10 Based on the sequence of class I, type 1 PREQ1 riboswitch aptamer from T. tengcongensis Figure 3 BLAST search results for E. coli tRNA Gln .

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


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4489241

( B ) J4/5 domain of the Tetrahymena ribozyme (PDB ID: 1GID), contains two AA sheared base pairs that are mutated to an AU and an AC base pair.

Next, we applied RNA-Redesign to the J4/5 motif from the P4-P6 domain of group I Tetrahymena ribozyme (PDB ID: 1GID), which forms contacts in the ribozyme's core ( 19 ).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4495719

( A ) P4–P6 domain: M 2 /Rosetta model (left), 38.3 Å root-mean-squared-deviation (RMSD); crystal structure (PDB ID 1GID, center left); M 2 /MOHCA-seq/Rosetta (MCM) model (center right... , 8.6 Å RMSD.

The following previously published datasets were used: Cate JH , Gooding AR , Podell E , Zhou K , Golden BL , Kundrot CE , Cech TR , Doudna JA , 1996 , Crystal structure of a group I ribozyme domain: principles of RNA packing , http://www.rcsb.org/pdb/explore/explore.do?structureId=1GID , Publicly available at RCSB Protein Data Bank (Accession No: 1GID).

Publication Year: 2015