메뉴 건너뛰기




Volumn 26, Issue 7, 2016, Pages 822-837

CryoEM structure of yeast cytoplasmic exosome complex

Author keywords

cryo EM; exosome; RNA decay; Rrp6; Ski7

Indexed keywords

EXOSOME MULTIENZYME RIBONUCLEASE COMPLEX; PROTEIN BINDING; RNA; RRP6 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; SKI7 PROTEIN, S CEREVISIAE;

EID: 84968547855     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2016.56     Document Type: Article
Times cited : (37)

References (47)
  • 1
    • 0030702085 scopus 로고    scopus 로고
    • The exosome: A conserved eukaryotic RNA processing complex containing multiple 3′5′ exoribonucleases
    • Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′ 5′ exoribonucleases. Cell 1997; 91:457-466.
    • (1997) Cell , vol.91 , pp. 457-466
    • Mitchell, P.1    Petfalski, E.2    Shevchenko, A.3    Mann, M.4    Tollervey, D.5
  • 2
    • 36049041612 scopus 로고    scopus 로고
    • RNA quality control in eukaryotes
    • Doma MK, Parker R. RNA quality control in eukaryotes. Cell 2007; 131:660-668.
    • (2007) Cell , vol.131 , pp. 660-668
    • Doma, M.K.1    Parker, R.2
  • 6
    • 33845407784 scopus 로고    scopus 로고
    • Reconstitution, activities, and structure of the eukaryotic RNA exosome
    • Liu Q, Greimann JC, Lima CD. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 2006; 127:1223-1237.
    • (2006) Cell , vol.127 , pp. 1223-1237
    • Liu, Q.1    Greimann, J.C.2    Lima, C.D.3
  • 7
    • 55549093442 scopus 로고    scopus 로고
    • Crystal structure of Escherichia coli PNPase: Central channel residues are involved in processive RNA degradation
    • Shi Z, Yang WZ, Lin-Chao S, Chak KF, Yuan HS. Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. RNA 2008; 14:2361-2371.
    • (2008) RNA , vol.14 , pp. 2361-2371
    • Shi, Z.1    Yang, W.Z.2    Lin-Chao, S.3    Chak, K.F.4    Yuan, H.S.5
  • 8
    • 70350336247 scopus 로고    scopus 로고
    • The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation
    • Bonneau F, Basquin J, Ebert J, Lorentzen E, Conti E. The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 2009; 139:547-559.
    • (2009) Cell , vol.139 , pp. 547-559
    • Bonneau, F.1    Basquin, J.2    Ebert, J.3    Lorentzen, E.4    Conti, E.5
  • 9
    • 84872131987 scopus 로고    scopus 로고
    • Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states of the phosphorolytic reaction
    • Lorentzen E, Conti E. Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states of the phosphorolytic reaction. Archaea 2012; 2012:721869.
    • (2012) Archaea , vol.2012 , pp. 721869
    • Lorentzen, E.1    Conti, E.2
  • 10
    • 40849106786 scopus 로고    scopus 로고
    • Structure of the active subunit of the yeast exosome core, Rrp44: Diverse modes of substrate recruitment in the RNase II nuclease family
    • Lorentzen E, Basquin J, Tomecki R, Dziembowski A, Conti E. Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Mol Cell 2008; 29:717-728.
    • (2008) Mol Cell , vol.29 , pp. 717-728
    • Lorentzen, E.1    Basquin, J.2    Tomecki, R.3    Dziembowski, A.4    Conti, E.5
  • 11
    • 57749189164 scopus 로고    scopus 로고
    • Endonucleolytic RNA cleavage by a eukaryotic exosome
    • Lebreton A, Tomecki R, Dziembowski A, Seraphin B. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 2008; 456:993-996.
    • (2008) Nature , vol.456 , pp. 993-996
    • Lebreton, A.1    Tomecki, R.2    Dziembowski, A.3    Seraphin, B.4
  • 12
    • 58149236691 scopus 로고    scopus 로고
    • The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities
    • Schaeffer D, Tsanova B, Barbas A, et al. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol 2009; 16:56-62.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 56-62
    • Schaeffer, D.1    Tsanova, B.2    Barbas, A.3
  • 13
    • 36749085158 scopus 로고    scopus 로고
    • Architecture of the yeast Rrp44-exosome complex suggests routes of RNA recruitment for 3' end processing
    • Wang H-W, Wang J, Ding F, et al. Architecture of the yeast Rrp44-exosome complex suggests routes of RNA recruitment for 3' end processing. Proc Natl Acad Sci USA 2007; 104:16844-16849.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 16844-16849
    • Wang, H.-W.1    Wang, J.2    Ding, F.3
  • 14
    • 84874742223 scopus 로고    scopus 로고
    • Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex
    • Makino DL, Baumgartner M, Conti E. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature 2013; 495:70-75.
    • (2013) Nature , vol.495 , pp. 70-75
    • Makino, D.L.1    Baumgartner, M.2    Conti, E.3
  • 16
    • 79960668648 scopus 로고    scopus 로고
    • Structural components and architectures of RNA exosomes
    • Januszyk K, Lima CD. Structural components and architectures of RNA exosomes. RNA exosome: Springer 2010:9-28.
    • (2010) RNA Exosome: Springer , pp. 9-28
    • Januszyk, K.1    Lima, C.D.2
  • 17
    • 84893752136 scopus 로고    scopus 로고
    • Visualization of distinct substrate-recruitment pathways in the yeast exosome by em
    • Liu JJ, Bratkowski MA, Liu X, Niu CY, Ke A, Wang HW. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nat Struct Mol Biol 2014; 21:95-102.
    • (2014) Nat Struct Mol Biol , vol.21 , pp. 95-102
    • Liu, J.J.1    Bratkowski, M.A.2    Liu, X.3    Niu, C.Y.4    Ke, A.5    Wang, H.W.6
  • 18
    • 79960681216 scopus 로고    scopus 로고
    • Rrp6, rrp47 and cofactors of the nuclear exosome
    • Butler JS, Mitchell P. Rrp6, rrp47 and cofactors of the nuclear exosome. Adv Exp Med Biol 2010; 702:91-104.
    • (2010) Adv Exp Med Biol , vol.702 , pp. 91-104
    • Butler, J.S.1    Mitchell, P.2
  • 19
    • 84904821452 scopus 로고    scopus 로고
    • Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA
    • Wasmuth EV, Januszyk K, Lima CD. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA. Nature 2014; 511:435-439.
    • (2014) Nature , vol.511 , pp. 435-439
    • Wasmuth, E.V.1    Januszyk, K.2    Lima, C.D.3
  • 21
    • 0035801392 scopus 로고    scopus 로고
    • Ski7p G protein interacts with the exosome and the Ski complex for 3′-to-5′ mRNA decay in yeast
    • Araki Y, Takahashi S, Kobayashi T, Kajiho H, Hoshino Si, Katada T. Ski7p G protein interacts with the exosome and the Ski complex for 3′-to-5′ mRNA decay in yeast. EMBO J 2001; 20:4684-4693.
    • (2001) EMBO J , vol.20 , pp. 4684-4693
    • Araki, Y.1    Takahashi, S.2    Kobayashi, T.3    Kajiho, H.4    Si, H.5    Katada, T.6
  • 22
    • 84882796823 scopus 로고    scopus 로고
    • The yeast ski complex: Crystal structure and RNA channeling to the exosome complex
    • Halbach F, Reichelt P, Rode M, Conti E. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell 2013; 154:814-826.
    • (2013) Cell , vol.154 , pp. 814-826
    • Halbach, F.1    Reichelt, P.2    Rode, M.3    Conti, E.4
  • 23
    • 84936847213 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae Ski7 Is a GTP-binding protein adopting the characteristic conformation of active translational GTPases
    • Kowalinski E, Schuller A, Green R, Conti E. Saccharomyces cerevisiae Ski7 Is a GTP-binding protein adopting the characteristic conformation of active translational GTPases. Structure 2015; 23:1336-1343.
    • (2015) Structure , vol.23 , pp. 1336-1343
    • Kowalinski, E.1    Schuller, A.2    Green, R.3    Conti, E.4
  • 24
    • 84862991581 scopus 로고    scopus 로고
    • Elastic coupling between RNA degradation and unwinding by an exoribonuclease
    • Lee G, Bratkowski MA, Ding F, Ke A, Ha T. Elastic coupling between RNA degradation and unwinding by an exoribonuclease. Science 2012; 336:1726-1729.
    • (2012) Science , vol.336 , pp. 1726-1729
    • Lee, G.1    Bratkowski, M.A.2    Ding, F.3    Ke, A.4    Ha, T.5
  • 25
    • 84861841297 scopus 로고    scopus 로고
    • Translation drives mRNA quality control
    • Shoemaker CJ, Green R. Translation drives mRNA quality control. Nat Struct Mol Biol 2012; 19:594-601.
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 594-601
    • Shoemaker, C.J.1    Green, R.2
  • 26
    • 0037155584 scopus 로고    scopus 로고
    • Exosome-mediated recognition and degradation of mRNAs lacking a termination codon
    • van Hoof A, Frischmeyer PA, Dietz HC, Parker R. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 2002; 295:2262-2264.
    • (2002) Science , vol.295 , pp. 2262-2264
    • Van Hoof, A.1    Frischmeyer, P.A.2    Dietz, H.C.3    Parker, R.4
  • 27
    • 84867618518 scopus 로고    scopus 로고
    • Degradation of mRNAs that lack a stop codon: A decade of nonstop progress
    • Klauer AA, van Hoof A. Degradation of mRNAs that lack a stop codon: a decade of nonstop progress. Wiley Interdiscip Rev RNA 2012; 3:649-660.
    • (2012) Wiley Interdiscip Rev RNA , vol.3 , pp. 649-660
    • Klauer, A.A.1    Van Hoof, A.2
  • 28
    • 79958809003 scopus 로고    scopus 로고
    • Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome
    • Becker T, Armache JP, Jarasch A, et al. Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome. Nat Struct Mol Biol 2011; 18:715-720.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 715-720
    • Becker, T.1    Armache, J.P.2    Jarasch, A.3
  • 29
    • 79960473450 scopus 로고    scopus 로고
    • Activities of human RRP6 and structure of the human RRP6 catalytic domain
    • Januszyk K, Liu Q, Lima CD. Activities of human RRP6 and structure of the human RRP6 catalytic domain. RNA 2011; 17:1566-1577.
    • (2011) RNA , vol.17 , pp. 1566-1577
    • Januszyk, K.1    Liu, Q.2    Lima, C.D.3
  • 30
    • 0032579440 scopus 로고    scopus 로고
    • Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications
    • Brachmann CB, Davies A, Cost GJ, et al. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 1998; 14:115-132.
    • (1998) Yeast , vol.14 , pp. 115-132
    • Brachmann, C.B.1    Davies, A.2    Cost, G.J.3
  • 31
    • 33845332754 scopus 로고    scopus 로고
    • EMAN2: An extensible image processing suite for electron microscopy
    • Tang G, Peng L, Baldwin PR, et al. EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 2007; 157:38-46.
    • (2007) J Struct Biol , vol.157 , pp. 38-46
    • Tang, G.1    Peng, L.2    Baldwin, P.R.3
  • 33
    • 80355128077 scopus 로고    scopus 로고
    • Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method
    • Liu X, Wang HW. Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method. J Vis Exp 2011; 49:e2574.
    • (2011) J Vis Exp , vol.49 , pp. e2574
    • Liu, X.1    Wang, H.W.2
  • 34
    • 84946482375 scopus 로고    scopus 로고
    • Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage
    • Li X, Zheng S, Agard DA, Cheng Y. Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage. J Struct Biol 2015; 192:174-178.
    • (2015) J Struct Biol , vol.192 , pp. 174-178
    • Li, X.1    Zheng, S.2    Agard, D.A.3    Cheng, Y.4
  • 35
    • 0038441501 scopus 로고    scopus 로고
    • Accurate determination of local defocus and specimen tilt in electron microscopy
    • Mindell JA, Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 2003; 142:334-347.
    • (2003) J Struct Biol , vol.142 , pp. 334-347
    • Mindell, J.A.1    Grigorieff, N.2
  • 36
    • 84868444740 scopus 로고    scopus 로고
    • RELION: Implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres SH. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 2012; 180:519-530.
    • (2012) J Struct Biol , vol.180 , pp. 519-530
    • Scheres, S.H.1
  • 37
    • 84866117936 scopus 로고    scopus 로고
    • Identification of cross-linked peptides from complex samples
    • Yang B, Wu YJ, Zhu M, et al. Identification of cross-linked peptides from complex samples. Nat Medthods 2012; 9:904-906.
    • (2012) Nat Medthods , vol.9 , pp. 904-906
    • Yang, B.1    Wu, Y.J.2    Zhu, M.3
  • 38
    • 42949089487 scopus 로고    scopus 로고
    • Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
    • Trabuco LG, Villa E, Mitra K, Frank J, Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 2008; 16:673-683.
    • (2008) Structure , vol.16 , pp. 673-683
    • Trabuco, L.G.1    Villa, E.2    Mitra, K.3    Frank, J.4    Schulten, K.5
  • 39
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera - A visualization system for exploratory research and analysis
    • Pettersen EF, Goddard TD, Huang CC et al. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 2004; 25:1605-1612.
    • (2004) J Comput Chem , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1    Goddard, T.D.2    Huang, C.C.3
  • 40
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Bashford D, Bellott M et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102:3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Bellott, M.3
  • 41
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • MacKerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004; 25:1400-1415.
    • (2004) J Comput Chem , vol.25 , pp. 1400-1415
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 42
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005; 26:1781-1802.
    • (2005) J Comput Chem , vol.26 , pp. 1781-1802
    • Phillips, J.C.1    Braun, R.2    Wang, W.3
  • 43
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 1995; 103:4613-4621.
    • (1995) J Chem Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 44
  • 45
    • 1842532008 scopus 로고    scopus 로고
    • A hierarchical approach to all-atom protein loop prediction
    • Jacobson MP, Pincus DL, Rapp CS, et al. A hierarchical approach to all-atom protein loop prediction. Proteins 2004; 55:351-367.
    • (2004) Proteins , vol.55 , pp. 351-367
    • Jacobson, M.P.1    Pincus, D.L.2    Rapp, C.S.3
  • 46
    • 0029831680 scopus 로고    scopus 로고
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    • Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng 1996; 9:1063.
    • (1996) Protein Eng , vol.9 , pp. 1063
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3
  • 47
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000; 16:404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.