Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 7

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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Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.

(2008) BMC Plant Biol 8

PubMed: 18631376 | PubMedCentral: PMC2488346 | DOI: 10.1186/1471-2229-8-79

Table 1 Products of mRNAs undergoing conversion editing Protein Name # of genes # of edited nucleotide sites PDB ID (chain) Transcription machinery  RNA polymease α 2 24 (2:21:1) 2a69 ... A), 1coo (_)  RNA polymerase β 1 19 (6:13:0) 2a69 (C)  RNA polymerase β' 2 20 (9:11:0) 2a69 (D) Translation machinery  ribosomal protein S1 2 6 (1: 5: 0)  ribosomal protein S2 4 34 (12: 22: 0) 2j00 (B)  ribosomal protein S3 7 74 (20: 32: 22) 2j00 (C)  ribosomal protein S4 4 52 (18:30:4) 2j00 (D)  ribosomal protein S7 4 9 (2:7:0)  ribosomal protein S8 1 2 (1: 1: 0) 2j00 (H)  ribosomal protein S10 2 5 (2: 3: 0) 2j00 (J)  ribosomal protein S12 3 21 (4: 14: 3) 2j00 (L)  ribosomal protein S13 3 18 (5: 12: 1) 2j00 (M)  ribosomal protein S14 3 5 (1:3:1) 2j00 (N)  ribosomal protein S19 5 33 (7:19:7) 2j00 (S)  ribosomal protein L2 4 10 (3:4:3) 2j01 (D)  ribosomal protein L5 5 28 (8:20:0) 2j01 (G)  ribosomal protein L14 1 1 (1:0:0) 2j01 (O)  ribosomal protein L16 4 33 (6:19:8) 2j01 (Q)  ribosomal protein L20 1 3 (1:2:0) 2j01 (U)  ribosomal protein L21 1 2 (2:0:0) 2j01 (V)  ribosomal protein L22 1 2 (0:2:0) 2j01 (W)  ribosomal protein L23 1 3 (0:3:0) 2j01 (X)  ribosomal protein L33 1 1 (0:1:0) 2j01 (6)  ribosomal protein L36 1 1 (0:1:0)  translation initiation factor 1 1 3 (1:2:0) 1hr0 (W)  Clp protease proteolytic subunit 1 1 6 (0:6:0) 1yg6 (A) Respiratory machinery  NADH dehydrogenase subunit J 1 2 (0:2:0) 2fug (5)  NADH dehydrogenase subunit K 1 3 (1:1:1) 2fug (6)  NADH dehydrogenase subunit I 1 2 (1:1:0) 2fug (9)  NADH dehydrogenase subunit 1 23 141 (71:60:10)  NADH dehydrogenase subunit 2 25 236 (55:147:34)  NADH dehydrogenase subunit 3 7 102 (36:62:4)  NADH dehydrogenase subunit 4 10 111 (31:77:3)  NADH dehydrogenase subunit 4L 9 64 (15:48:1)  NADH dehydrogenase subunit 5 7 180 (44:94:42)  NADH dehydrogenase subunit 6 5 61 (14:40:7)  NADH dehydrogenase subunit 7 4 86 (20:49:17)  NADH dehydrogenase subunit 9 6 58 (24:33:1)  cytochrome bc 1 complex cytochrome b 7 136 (68:59:9) 1kyo (C)  cytochrome c biogenesis ccmC 5 156 (65:77:14)  cytochrome c biogenesis ccmF 15 195 (90:88:17)  cytochrome c biogenesis ccsA 1 12 (2:10:0)  cytochrome c ccmB 7 278 (108:145:25)  cytochrome c oxidase I 20 324 (107:196:21) 1v55 (A)  cytochrome c oxidase II 14 164 (64:85:15) 1v55 (B)  cytochrome c oxidase III 15 155 (42:82:31) 1v55 (C) Photosynthesis machinery  photochlorophyllide reductase subunit chlL 1 9 (5:4:0) 2afh (E)  photochlorophyllide reductase subunit chlB 8 23 (10:13:0)  photochlorophyllide reductase subunit chlN 1 3 (1:2:0)  photosystem II subunit V 2 5 (1:3:1) 2axt (E)  photosystem II subunit VI 2 7 (1:5:1) 2axt (F)  photosystem II CP47 protein 2 55 (15:34:6) 2axt (B)  photosystem II H protein 1 4 (0:4:0) 2axt (H)  photosystem II J protein 1 2 (1:1:0) 2axt (J)  photosystem II L protein 4 8 (1:7:0) 2axt (L)  photosystem II M protein 1 1 (0:1:0) 2axt (M)  photosystem II N protein 1 2 (0:2:0)  photosystem II T protein 2 5 (2:3:0) 2axt (T)  photosystem II Z protein 1 1 (0:0:1) 2axt (Z)  cytochrome b 6 f complex petG 1 1 (0:1:0) 1vf 5(G)  cytochrome b 6 f complex petL 1 2 (1:1:0) 1vf5 (E)  cytochrome b 6 f subunit 4 2 19 (4:15:0) 1vf5 (B)  cytochrome f 1 2 (2:0:0) 1vf5 (C)  photosystem I P700 apoprotein A1 1 1 (1:0:0) 1jb0 (A)  photosystem I P700 apoprotein A2 1 1 (0:1:0) 1jb0 (B)  photosystem I subunit IX 1 1 (0:1:0) 1jb0 (J)  photosystem I assembly protein Ycf3 2 9 (2:7:0)  ATPase α 21 100 (66:28:6) 2ck3 (A)  ATPase β 1 7 (1:6:0) 2ck3 (D)  ATPase ε 1 3 (1:2:0) 1fs0 (E)  ATP synthase CF0 A chain 1 11 (2:8:1)  ATP synthase CF0 B chain 1 1 (0:1:0)  ATP synthase CF0 C chain 1 7 (1:6:0)  ATP synthase subunit 6 12 38 (19:17:2)  ATP synthase subunit 9 10 58 (17:37:4)  RUBISCO large subunit 5 35 (11:23:1) 1uw9 (A) Other machinery  Chloroplast envelope membrane protein 1 5 (3:2:0)  Acetyl-coA carboxylase carboxyl transferase β 1 16 (6:9:1) 2f9i (B)  succinate dehydrogenase subunit 4 1 1 (0:1:0)  maturase K (intron-encoded protein) 1 4 (0:4:0)  maturase R (intron-encoded protein) 5 54 (13:36:5) Hypothetical organelle proteins  hypothetical protein ycf1 1 2 (0:1:1)  hypothetical protein ycf2 1 7 (4:2:1)  hypothetical protein ymf19 5 20 (4:8:8)  orf114 1 2 (0:0:2)  orf240a 1 1 (1:0:0)  orf25 5 45 (8:33:4)  orfX 4 101 (45:45:11) Total 365 3560 1219 1983 358 Detail of the data is described in Additional files 1 and 2 .

Publication Year: 2008


Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily.

(2009) Int J Mol Sci 10

PubMed: 19564956 | PubMedCentral: PMC2695284 | DOI: 10.3390/ijms10052412

Of the 95 domains classified as OB-fold motifs in SCOP, six structures (1CKM, 1HR0, 1J5E_L, 1J5E_Q, 1MIU, 1X9N) were discarded because of low resolution and/or errors, including two structures that ha... a knot in the main-chain (1X9N and 1CKM).

Publication Year: 2009


Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.

(2009) Nucleic Acids Res 37

PubMed: 19561193 | PubMedCentral: PMC2731904 | DOI: 10.1093/nar/gkp519

( A–D ) Cleavages in 18S rRNA mapped onto 16S rRNA in the T. thermophilus 30S subunit crystal structure (18: PDB code 1HR0) from the OB subdomain (A), the C-terminal helical domain (B), the NT... (C), or the CTT (D).

Modeling The eIF1A/40S ribosomal subunit interaction was modeled using the crystal structures of the T. thermophilus 30S subunit in complex with IF1 (18: PDB code 1HR0) and of the 70S ribosome in complex with mRNA and tRNAs (24: PDB code 1JGO; 25: PDB code 1JGP), and the NMR structure of human eIF1A (15: PDB code 1D7Q).

Publication Year: 2009


Initiation factor eIF2? promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.

(2011) Nat Struct Mol Biol 18

PubMed: 22002225 | PubMedCentral: PMC3210414 | DOI: 10.1038/nsmb.2133

aIF2α is from the aIF2αγ heterodimer structure (pdb code: 2AHO 15 ); eIF1 is from the 40S–eIF1 co-crystal structure (pdb code: 2XZM 17 ); and eIF1A (pdb code: 1D7Q) was... positioned based on the bacterial 30S–IF1 structure (pdb code: 1HR0 9 ) and hydroxyl radical mapping data 8 .

Publication Year: 2011


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 molecules 1HR0, 1I96 and 1XMO contain a putative module (residue numbers 805–808/830–847, 808–811/833–850 and 805–808/830–847, respecti... ely) with the same structure ( < ((&))) ………… ).)

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


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).

Publication Year: 2005