Primary Citation PubMed: 23376952
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Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 24189234 | PubMedCentral: PMC3817696 | DOI: 10.1107/S0907444913011438
Figure 5 Surface representation of the final refined structure of the yeast exosome complex with the bound RNA in black (PDB entry 4ifd ; Makino, Baumgärtner et al. , 2013 ▶ ).
The PDB code for this structure is 4ifd .
Supplementary Material PDB reference: 11-subunit exosome in complex with RNA, 4ifd This work was funded by the Max Planck Gesellschaft, ERC Advanced Investigator Grant 294371 and the Deutsche Forschungsgemeinschaft (SFB646, SFB1035, GRK1721 and CIPSM) to EC.
Publication Year: 2013
Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM.
(2014) Nat Struct Mol Biol 21
PubMed: 24336220 | PubMedCentral: PMC3976988 | DOI: 10.1038/nsmb.2736
( c ) Docking of the 13nt-ssRNA substrate of the atomic model of Rrp44 RNB domain in complex with ssRNA (PDB: 4IFD) 18 into the RE-short 3D model, mimicking the direct-access route.
For the RE-long 3D reconstruction, we took the recently published crystal structure of the yeast RE in complex with a partial hairpin RNA substrate (PDB 4IFD) 18 and docked it in the map as a rigid body.
Publication Year: 2014
PubMed ID is not available.
Published in 2014
b , The structure of yeast Rrp44 extracted from the 11 subunit RNA exosome 20 (PDB 4IFD).
Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.
(2014) Nature 511
PubMed: 25043052 | PubMedCentral: PMC4310248 | DOI: 10.1038/nature13406
b, Superposed structures of the Rrp6 CTD from Exo10 Rrp6 (residues 525-628; teal) and Exo10 Rrp44+Rrp6Cterm (residues 532-557, 565-619; magenta; PDB 4IFD) reveal overall similarity for residues within... the respective models.
RNA from PDB 4IFD was edited to remove the stem loop after nt 36.
Extended Data Figure 8 RNA paths to Rrp6 and Rrp44 Structure of an Exo11 Rrp44/Rrp6 model derived by superposing the PH-like ring subunits in Exo10 Rrp6 and Exo10 Rrp44+6Cterm (PDB 4IFD).
Subunits and surfaces depicted as in (a) with the exception that the RNA is now derived from the structure of Exo10 Rrp44+6Cterm (PDB 4IFD) with the RNA edited to remove the stem loop after nucleotide 36.
The structure solved by molecular replacement using Phaser 32 and coordinates of human apo Exo9 (PDB: 2NN6) and yeast Rrp6 CAT (PDB: 2HBL) as search models followed by docking yeast Exo10 Rrp44+6Cterm (PDB: 4IFD) ( Extended Data Table 1 ).
Published in 2015
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
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