Citations in PubMed

Primary Citation PubMed: 12242451 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

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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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


Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.

(2008) Nucleic Acids Res 36

PubMed: 18854351 | PubMedCentral: PMC2582612 | DOI: 10.1093/nar/gkn657

The crystal structures represent four phases of one cycle of nucleotide addition during the elongation phase of transcription: the pre-insertion substrate complex, the insertion substrate complex, the... pre-translocation product complex and the post-translocation complex with PDB codes 1S0V ( 41 ), 1S76 ( 42 ), 1S77 ( 42 ) and 1MSW ( 43 ), respectively.

Publication Year: 2008


A tool for calculating binding-site residues on proteins from PDB structures.

(2009) BMC Struct Biol 9

PubMed: 19650927 | PubMedCentral: PMC2728722 | DOI: 10.1186/1472-6807-9-52

Upon the input, the TCBRP automatically finds all PDB structures that contain T7 RNA polymerase, i.e. 1ARO , 1QLN , 2PI4 , 1S76 , 1MSW , 1CEZ , 1S77 , and 2PI5 .

Publication Year: 2009


Robust probabilistic superposition and comparison of protein structures.

(2010) BMC Bioinformatics 11

PubMed: 20594332 | PubMedCentral: PMC2912885 | DOI: 10.1186/1471-2105-11-363

Table 1 Marginal likelihood of different models Protein PDB IDs Student t K Laplace Gauss GroEL 1AON - 1OEL -4328.57 -4307.22 -5132.84 -5722.35 DNA Pol 1IH7 - 1IG9 -5574.80 -5750.12 -6340.01 -8011.05 ... AN 1RRP - 1BYU -1124.86 -1176.53 -1795.92 -2286.10 Topo II 1BGW - 1BJT -4496.17 -4553.50 -7210.74 -8042.00 Pneumolysin 2BK2 - 2BK1 -2692.73 -2465.09 -5195.85 -5491.90 ER 3ERD - 3ERT -538.11 -622.69 -1290.81 -1980.96 RNA Pol 1QLN - 1MSW -5296.61 -5455.79 -8471.69 -10168.07 Adenylate Kinase 1AKE - 4AKE -1499.73 -1502.75 -1685.11 -2000.35 Myosin 1B7T - 1DFK -4819.91 -5046.02 -6380.11 -7701.83 Synthetic data Student t -9179.46 -9253.48 -12465.97 -13951.94 Synthetic data Gauss -5108.73 -5112.43 -5077.97 -5115.98 Logarithm of the marginal likelihood P ( M | D ) of the different displacement models obtained for nine structure pairs undergoing domain movements.

Publication Year: 2010


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


Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.

(2013) Nucleic Acids Res 41

PubMed: 23275546 | PubMedCentral: PMC3561941 | DOI: 10.1093/nar/gks1251

Viral species and PDB structures used as queries in this study Queries Abbreviations PDB Length of structure Picornaviridae, RdRp, +ssRNA     Poliovirus PV 1RA6 ( 3 ) 4... 1     Poliovirus (open) PV 3OL6 ( 9 ) 471     Poliovirus (closed) PV 3OL7 ( 9 ) 471     Coxsackie virus COXV 3DDK ( 11 ) 462     Human rhinovirus HRV 1XR6 ( 12 ) 460     Human rhinovirus HRV 1XR7 ( 12 ) 460     Foot and mouth disease virus FMDV 1U09 ( 2 ) 476 Caliciviridae, RdRp, +ssRNA     Norwalk virus NV 1SH0 ( 13 ) 510     Rabbit hemorrhagic disease virus RHDV 1KHV ( 14 ) 516     Rabbit hemorrhagic disease virus RHDV 1KHW ( 14 ) 516     Sapporo virus SAPV 2CKW ( 15 ) 515 Flaviviridae, RdRp, +ssRNA     Hepatitis C virus HCV 1NB4 ( 16 ) 570     Hepatitis C virus HCV 1NB7 ( 16 ) 570     Bovine viral diarrhea virus BVDV 1S48 ( 17 ) 609     West Nile (Kunjin) virus WNV 2HCS ( 18 ) 595     Dengue virus DENV 2J7U ( 19 ) 635 Cystoviridae, RdRp, dsRNA     Bacteriophage Phi6 PHI6 1HHS ( 20 ) 664     Bacteriophage Phi6 PHI6 1HI0 ( 20 ) 664 Reoviridae, RdRp, dsRNA     Reovirus lambda 3 REOV 1MUK ( 21 ) 1267     Reovirus lambda 3 REOV 1N35 ( 21 ) 1267     Rotavirus ROTAV 2R7X ( 22 ) 1095 Birnaviridae, RdRp, dsRNA     Infectious bursal disease, birnavirus IBDV 2PGG ( 5 ) 774     Infectious pancreatic necrosis IPNV 2YI8 ( 23 ) 799     Infectious pancreatic necrosis IPNV 2YI9 ( 23 ) 799     Infectious pancreatic necrosis IPNV 2YIA ( 23 ) 799 RdDp     HIV1 HIV1 1RT1 ( 24 ) 560     HIV1 (closed) HIV1 1RTD ( 25 ) 554     HIV1 (open) HIV1 2HMI ( 26 ) 558     Tribolium castaneum TERT 3DU6 ( 27 ) 596 DdRp     Bacteriophage T7 (closed) T7 RNAP 1S77 ( 28 ) 883     Bacteriophage T7 (closed) T7 RNAP 2AJQ ( 29 ) 704     Bacteriophage T7 (open) T7 RNAP 1MSW ( 30 ) 883     Bacteriophage N4 N4 3C2P ( 31 ) 1117 DdDp     Thermus aquaticus (open) TAQ 2KTQ ( 32 ) 538     Thermus aquaticus (closed) TAQ 3KTQ ( 32 ) 540     Thermus aquaticus (open) TAQ 4KTQ ( 32 ) 539     Bacteriophage T7 T7 DNAP 1T7P ( 33 ) 698 Queries of both open and closed structures were used to assess the impact of this feature on R2R correspondence.

Publication Year: 2013


Computational simulation strategies for analysis of multisubunit RNA polymerases.

(2013) Chem Rev 113

PubMed: 23987500 | PubMedCentral: PMC3829680 | DOI: 10.1021/cr400046x

Table 2 Structures of Bacteriophage T7 RNA Polymerase PDB ID resolution (Å) nucleic acid nucleotide state refs 3E2E 3.00 T/N/R   posttranslocation ( 83b ) 3E3J 6.70 T/N/R   pre... ranslocation ( 83b ) 2PI4 2.50 T/N GTP initiation ( 87 ) 2PI5 2.90 T/N   initiation ( 87 ) 1S76 2.88 T/N/R ATP posttranslocation ( 71 ) 1S77 2.69 T/N/R PP i pretranslocation ( 71 ) 1S0V 3.20 T/N/R ATP posttranslocation ( 88 ) 1H38 2.9 T/N/R   preinsertion ( 89 ) 1MSW 2.10 T/N/R   pretranslocation ( 82a ) 1QLN 2.40 T/N/R   preinsertion ( 90 ) 1CEZ 2.40 T/N   initiation ( 91 ) 1ARO 2.80     with inhibitor T7 lysozyme ( 92 ) 4RNP 3.00       ( 93 ) TEC structures have open and closed conformations.

Publication Year: 2013


Structure of human mitochondrial RNA polymerase elongation complex.

(2013) Nat Struct Mol Biol 20

PubMed: 24096365 | PubMedCentral: null | DOI: 10.1038/nsmb.2683

The NTD of T7 RNAP (a) is refolded in the elongation complex (PDB 1MSW 34 ), whereas the NTD of mtRNAP (b) is not, and resembles the NTD in the T7 intermediate (PDB 3E2E 15 ) (c) .

Publication Year: 2013


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