Citations in PubMed

Primary Citation PubMed: 11779468 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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The structure and function of small nucleolar ribonucleoproteins.

(2007) Nucleic Acids Res 35

PubMed: 17284456 | PubMedCentral: PMC1865073 | DOI: 10.1093/nar/gkl1172

Crystal structures of ( A ) the archaeal H/ACA Ψ synthase Cbf5 (2APO) and ( B ) the E. coli tRNA Ψ synthase TruB (1K8W).

Publication Year: 2007

Dissecting protein-RNA recognition sites.

(2008) Nucleic Acids Res 36

PubMed: 18353859 | PubMedCentral: PMC2377425 | DOI: 10.1093/nar/gkn102

The protein–RNA data set A. Complexes with tRNA ( 21 )     1asy 1c0a 1f7u* 1ffy* 1gax 1h3e 1h4s 1j1u* 1n78* 1qf6 1qtq 1ser     1... tt 1u0b* 1vfg 2azx 2bte 2csx 2drb 2fk6 2fmt B. Ribosomal proteins ( 11 )     1dfu* 1f7y 1feu* 1g1x 1i6u 1mji 1mms 1mzp 1s03 1sds* 2hw8* C. Duplex RNA ( 17 )     1di2* 1e7k 1hq1* 1msw* 1ooa 1r3e* 1rpu 1si3 1wne 1yvp* 1zbi* 2az0     2ez6* 2f8s 2gjw 2hvy* 2ipy D. Single-stranded RNA ( 30 )     1a9n 1av6 1cvj 1g2e* 1jbs* 1jid* 1k8w* 1knz 1kq2 1lng* 1m5o* 1m8v     1m8w* 1n35 1wpu* 1wsu* 1zbh 1zh5* 2a8v 2anr* 2asb* 2b3j* 2bx2 2db3*     2f8k* 2g4b 2gic 2i82* 2ix1 2j0s* E. Miscellaneous ( 2 )     2bgg* 2bh2* Asterisk indicates PDB entry with resolution better than 2.4 Å.

Publication Year: 2008

DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.

(2011) BMC Bioinformatics 12

PubMed: 21851628 | PubMedCentral: PMC3179970 | DOI: 10.1186/1471-2105-12-348

There are 72 protein-RNA complexes in the training set taken from crystal structures of protein-RNA complexes downloaded from the Protein Data Bank (PDB codes: 1a1v , 1a34 , 1b2m , 1c0a , 1d9d , 1dfu ... 1di2 , 1bu1 , 1ec6 , 1f7u , 1feu , 1ffy , 1fxl , 1gtf , 1gtr , 1hq1 , 1j1u , 1jbs , 1jid , 1jj2 - 50S ribosome structure, 1k8w , 1knz , 1lng , 1m8w , 1mji , 1msw , 1n35 , 1n78 , 1ooa , 1qln , 1r3e , 1r9f , 1rc7 , 1sds , 1tfw , 1u0b , 1urn , 1uvj , 1wsu , 1yvp , 1zbi , 1a8v , 2bgg , 2bh2 ) [ 25 ].

Publication Year: 2011

A coarse-grained force field for Protein-RNA docking.

(2011) Nucleic Acids Res 39

PubMed: 21846771 | PubMedCentral: PMC3241652 | DOI: 10.1093/nar/gkr636

Results for docking with unbound structures Complex Receptor Ligand br:bl ur:bl br:ul ur:ul 1DFU mn : p 364D abc (2.8) 1B75 (3.8) 3 1 −[18] −[4] 1JBR d : b 430D a (2.8) 1AQZ a (0.6) 14... 18 30[2] 100 1K8W b : a 2K4C (2.8) 1R3F a (1.5) 1 – 2[1] – 1TTT d : a 6TNA a (2.6) 1TUI a (10.1) 1 −[480] 291 – 2RKJ c : a , b 1Y0Q a (2.6) 1Y42 aa (1.1) 2 −[13] −[>1k] −[>1k] 2AZ2 cd : ab model (1.4) 2B9Z (1.5) 3 3[1] >1k[349] >1k[43] 2E9T bc : a model (3.3) 1U09 a (0.8) 2 −[712] >1k −[-] Subscripts at PDB id denote involved chains, numbers in brackets correspond to RMSD (P atoms for receptor and Cα for ligand) versus bound structure (in case of multiple NMR models an average value is provided); br, bl, ur, ul—bound/unbound receptor/ligand; numbers correspond to the ranks of ‘hits’ or ‘acceptable’ solutions (in square brackets).

Publication Year: 2011

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

An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation.

(2014) Nucleic Acids Res 42

PubMed: 24371284 | PubMedCentral: PMC3973310 | DOI: 10.1093/nar/gkt1331

To account for the different structural states of TruB, TruB wild type was modeled in two functionally different conformations, its apo conformation as observed in crystal structures lacking RNA [PDBI... : 1R3F ( 26 )], as well as its conformation when bound to tRNA [PDBID: 1K8W ( 5 )].

To generate a starting structure for TruB-bound, the crystal structure for E. coli TruB bound to a short RNA [PDBID: 1K8W ( 5 )] and the TruB-apo model were used.

Water molecules within 10 Å of the protein as observed in the crystal structure (PDBID: 1K8W) were also included in the TruB-bound model.

Image was generated in VMD using PDBID: 1K8W.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4352265

Table 1 List of protein-RNA complexes used in the present study Complex Organism PDB code RMSD (Å) Sequence identity (%) Binding site residues Protein (%) RNA (%) Elongation Factor TU E. coli ... OB2:A 1.4 71 7.63 22.37 T. aquaticus 1OB5:A 9.14 20.78 Leucyl-tRNA synthetase E. coli 4ARC:A 1-2: 1.9 1-2: 45 4.09 25.29 T. thermophilus 2BTE:A 1–3: 2.5 1–3: 27 3.08 22.89 P. horikoshii 1WZ2:A 2–3: 1.6 2–3: 29 3.21 18.18 Retinoic acid inducible protein I A. platyrhynchos 4A36:A 2.6 59 4.14 28.95 H. sapiens 3TMI:A 3.17 42.86 Glutamyl-tRNA synthetase T. maritima 3AKZ:A 2.3 41 9.65 33.78 T. thermophilus 1N78:A 9.19 30.67 Aspartyl-tRNA synthetase E. coli 1IL2:A 1-2: 2.1 1-2: 49 7.12 32.00 T. thermophilus 1EFW:A 1–3: 2.2 1–3: 28 3.97 20.55 S. cerevisiae 1ASY:A 2–3: 2.3 2–3: 30 8.57 26.67 Signal recognition particle H. sapiens 1MFQ:C 1-2: 2.7 1-2: 36 9.30 6.25 M. jannaschii 2V3C:C 1–3: 5.4 1–3: 32 5.79 18.48 S. solfataricus 1QZW:A 2–3: 1.29 2–3: 48 2.50 11.70 ATP dependent RNA helicase H. sapiens 3G0H:A 1.1 51 5.19 100.00 S. cerevisiae 3PEY:A 5.57 83.33 Tyrosyl-tRNA synthetase S. cerevisiae 2DLC:X 1-2: 1.7 1-2: 35 2.79 5.26 M. jannaschii 1J1U:A 1–3: 2.7 1–3: 26 4.58 6.49 T. thermophilus 1H3E:A 2–3: 2.2 2–3: 27 4.63 16.28 Probable exosome complex exonuclease 1 A. fulgidus 3M7N:D 0.9 59 2.33 33.33 P. abyssi 2PO1:A 3.21 40.00 50S ribosomal protein L7Ae A. fulgidus 1RLG:A 0.8 60 13.45 36.00 M. jannaschii 1SDS:A 17.09 23.33 60S ribosomal protein L7 S. cerevisiae 3O5H:G 1.9 47 1.23 1.65 T. thermophila 4A1C:V 2.51 5.00 STAR family quaking protein C. elegans 4JVY:A 2.8 58 10.20 71.43 H. sapiens 4JVH:A 8.61 63.64 Retinoic acid inducible protein I A. platyrhynchos 4A2X:A 1.7 55 3.05 14.29 H. sapiens 3NCU:A 7.46 25.00 Arginyl-tRNA synthetase S. cerevisiae 1F7U:A 2.6 29 7.25 32.89 P. horikoshii 2ZUF:A 6.20 32.05 Pumilio mRNA binding factor S. cerevisiae 3 K49:A 1.1 45 9.49 90.00 H. sapiens 2YJY:A 7.43 90.00 tRNA pseudouridine synthase B E. coli 1K8W:A 1.8 34 11.31 54.55 T. maritime 1R3E:A 10.36 70.59 Signal recognition particle 19 kDa protein M. jannaschii 1LNG:A 2.1 34 35.82 16.49 S. solfataricus 3KTW:A 22.94 19.79 Phenylalanyl-tRNA synthetase T. thermophiles 2IY5:A 2.1 31 3.14 7.89 H. sapiens 3TUP:A 4.58 25.00 Identification of binding site residues Generally, binding site residues in protein-RNA complex structures have been identified with three different criteria: (i) distance between contacting atoms in protein and RNA using a specific cut-off value [ 18 , 19 ], (ii) reduction of solvent accessibility upon binding [ 20 ] and (iii) inter-residue interaction energy [ 21 ].

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4529986

Table 4 Protein-RNA complexes in RB344 dataset RNA category PDB ID RNAse 2BX2 2IX1 2NUG 2QKB 2XDB 2Y8Y 3BSU 3IAB 3T3O 3ULD 4 AM3 4ATO SRP 1E8O 1HQ1 1JID 1LNG 1MFQ 2V3C 3KTW Aptamer 1OOA 3AGV 3... D2 3V7E dsRNA 1DI2 2YKG 3CIY 3EQT 3LRR 4IG8 Exosome 2JEA 2PO1 2VNU 4IFD mRNA 1FXL 1GTF 1MSW 1UVM 1WPU 1WSU 1ZH5 2A8V 2F8K 2IPY 2J0S 2O5I 2PJP 2Q66 2VPL 2XGJ 2XNR 2XS2 2XZO 3BX2 3D2S 3I5X 3ICE 3MDI 3NMR 3P6Y 3PEY 3PO3 3Q0Q 3QGC 3R2C 3RER 4 F02 4HXH 4J7L 4JVY Ribosomal 1DFU 1FEU 1FKA 1HR0 1I6U 1JBS 1MJI 1MMS 1MZP 1NKW 1SDS 1T0K 1UN6 1VQ8 1VQO 1Y69 2ASB 2BH2 2D3O 2 J01 2QA4 2VQE 2XFZ 2ZJQ 2ZJR 3AEV 3DH3 3F1E 3HUW 3I8I 3IEV 3KIS 3MOJ 3OIN 3R8S 3R8T 3R9X 3SFS 3SGF 3UMY 3 V24 3 V26 3V2C 3V2D 3V2F 3ZN9 4DH9 4GD1 4JUW 4JUX Small 1SI3 1YVP 2BGG 2F8S 3A6P 3ADI 3HO1 3HTX 3 MJ0 3NMU 3NVI 3O7V 3VYX 3VYY 3ZC0 4F1N 4KRE snRNP 1M8V 1URN 2OZB Splicing 1A9N 2G4B tRNA 1ASY 1B23 1C0A 1F7U 1FFY 1GAX 1H3E 1H4S 1J1U 1J2B 1K8W 1 N78 1Q2R 1QF6 1QTQ 1R3E 1SER 1U0B 1VFG 1WZ2 2AZX 2B3J 2CT8 2CZJ 2D6F 2DER 2DLC 2DU3 2FK6 2FMT 2GJW 2I82 2IY5 2ZNI 2ZUE 2ZZM 3AL0 3 AM1 3AMT 3BT7 3EPH 3FOZ 3HL2 3ICQ 3KFU 3OVB 3QSY 3TUP 3VJR 3W3S 3ZGZ 4ARC Viral 1A34 1AV6 1DDL 1F8V 1HYS 1KNZ 1 N35 1PGL 1R9F 2AZ2 2BU1 2GIC 2GTT 2JLV 2QUX 2R7W 2W2H 2WJ8 2Z2Q 2ZI0 2ZKO 3AVX 3BSO 3KMQ 3 L25 3O8C 3RW6 3T5N 4FY7 4GV9 4H5P 4HKQ 4J1G 4K4Z Other 1EC6 2ANR 2DB3 2GJE 2GXB 2PY9 2R8S 2XLK 3AF6 3HAX 3IEM 3PF4 3PKM 3QJL 3RC8 3S14 4B3G 4ERD 4FXD 4GG4 4ILL PDB ID of protein-RNA complexes in RB344 dataset Identification of protein surface residues To determine protein surface residues, accessible areas will be computed first.

Publication Year: 2015