-
1
-
-
14244272868
-
PHENIX: Building new software for automated crystal-lographic structure determination
-
Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystal-lographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948-1954
-
(2002)
Acta Crystallogr D Biol Crystallogr
, vol.58
, pp. 1948-1954
-
-
Adams, P.D.1
Grosse-Kunstleve, R.W.2
Hung, L.W.3
Ioerger, T.R.4
McCoy, A.J.5
Moriarty, N.W.6
Read, R.J.7
Sacchettini, J.C.8
Sauter, N.K.9
Terwilliger, T.C.10
-
2
-
-
77954214431
-
Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein
-
Boland A, Tritschler F, Heimstädt S, Izaurralde E, Weichenrieder O (2010) Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein. EMBO Rep 11: 522-527
-
(2010)
EMBO Rep
, vol.11
, pp. 522-527
-
-
Boland, A.1
Tritschler, F.2
Heimstädt, S.3
Izaurralde, E.4
Weichenrieder, O.5
-
3
-
-
33947273235
-
Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
-
Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128: 1089-1103
-
(2007)
Cell
, vol.128
, pp. 1089-1103
-
-
Brennecke, J.1
Aravin, A.A.2
Stark, A.3
Dus, M.4
Kellis, M.5
Sachidanandam, R.6
Hannon, G.J.7
-
4
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905-921
-
(1998)
Acta Crystallogr D Biol Crystallogr
, vol.54
, pp. 905-921
-
-
Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
5
-
-
78650306521
-
Small RNA sorting: Matchmaking for Argonautes
-
Czech B, Hannon GJ (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12: 19-31
-
(2011)
Nat Rev Genet
, vol.12
, pp. 19-31
-
-
Czech, B.1
Hannon, G.J.2
-
6
-
-
70449127022
-
Hierarchical rules for Argonaute loading in Drosophila
-
Czech B, Zhou R, Erlich Y, Brennecke J, Binari R, Villalta C, Gordon A, Perrimon N, Hannon GJ (2009) Hierarchical rules for Argonaute loading in Drosophila. Mol Cell 36: 445-456
-
(2009)
Mol Cell
, vol.36
, pp. 445-456
-
-
Czech, B.1
Zhou, R.2
Erlich, Y.3
Brennecke, J.4
Binari, R.5
Villalta, C.6
Gordon, A.7
Perrimon, N.8
Hannon, G.J.9
-
8
-
-
70149116785
-
The 5 terminal uracil of let-7a is critical for the recruitment of mRNA to Argonaute2
-
Felice KM, Salzman DW, Shubert-Coleman J, Jensen KP, Furneaux HM (2009) The 5 terminal uracil of let-7a is critical for the recruitment of mRNA to Argonaute2. Biochem J 422: 329-341
-
(2009)
Biochem J
, vol.422
, pp. 329-341
-
-
Felice, K.M.1
Salzman, D.W.2
Shubert-Coleman, J.3
Jensen, K.P.4
Furneaux, H.M.5
-
9
-
-
77953479619
-
Structural basis for 5-nucleotide base-specific recognition of guide RNA by human AGO2
-
Frank F, Sonenberg N, Nagar B (2010) Structural basis for 5-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465: 818-822
-
(2010)
Nature
, vol.465
, pp. 818-822
-
-
Frank, F.1
Sonenberg, N.2
Nagar, B.3
-
10
-
-
44449096738
-
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells
-
Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler ELW, Zapp ML, Weng Z, Zamore PD (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320: 1077-1081
-
(2008)
Science
, vol.320
, pp. 1077-1081
-
-
Ghildiyal, M.1
Seitz, H.2
Horwich, M.D.3
Li, C.4
Du, T.5
Lee, S.6
Xu, J.7
Elw, K.8
Zapp, M.L.9
Weng, Z.10
Zamore, P.D.11
-
11
-
-
75649129754
-
Sorting of Drosophila small silencing RNAs partitions microRNA strands into the RNA interference pathway
-
Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD (2010) Sorting of Drosophila small silencing RNAs partitions microRNA strands into the RNA interference pathway. RNA 16: 43-56
-
(2010)
RNA
, vol.16
, pp. 43-56
-
-
Ghildiyal, M.1
Xu, J.2
Seitz, H.3
Weng, Z.4
Zamore, P.D.5
-
12
-
-
58449134534
-
Small silencing RNAs: An expanding universe
-
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10: 94-108
-
(2009)
Nat Rev Genet
, vol.10
, pp. 94-108
-
-
Ghildiyal, M.1
Zamore, P.D.2
-
13
-
-
70349476898
-
Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline
-
Gu W, Shirayama M, Conte D, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen C-CG, Chaves DA, Duan S, Kasschau KD, Fahlgren N, Yates JR, Mitani S, Carrington JC, Mello CC (2009) Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell 36: 231-244
-
(2009)
Mol Cell
, vol.36
, pp. 231-244
-
-
Gu, W.1
Shirayama, M.2
Conte, D.3
Vasale, J.4
Batista, P.J.5
Claycomb, J.M.6
Moresco, J.J.7
Youngman, E.M.8
Keys, J.9
Stoltz, M.J.10
Chen, C.-C.G.11
Chaves, D.A.12
Duan, S.13
Kasschau, K.D.14
Fahlgren, N.15
Yates, J.R.16
Mitani, S.17
Carrington, J.C.18
Mello, C.C.19
-
14
-
-
69949127421
-
Structural determinants of miRNAs for RISC loading and slicer-independent unwinding
-
Kawamata T, Seitz H, Tomari Y (2009) Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat Struct Mol Biol 16: 953-960
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 953-960
-
-
Kawamata, T.1
Seitz, H.2
Tomari, Y.3
-
15
-
-
80052303462
-
Multilayer checkpoints for microRNA authenticity during RISC assembly
-
Kawamata T, Yoda M, Tomari Y (2011) Multilayer checkpoints for microRNA authenticity during RISC assembly. EMBO Rep 12: 944-949
-
(2011)
EMBO Rep
, vol.12
, pp. 944-949
-
-
Kawamata, T.1
Yoda, M.2
Tomari, Y.3
-
16
-
-
44349103084
-
Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells
-
Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC, Siomi H (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453: 793-797
-
(2008)
Nature
, vol.453
, pp. 793-797
-
-
Kawamura, Y.1
Saito, K.2
Kin, T.3
Ono, Y.4
Asai, K.5
Sunohara, T.6
Okada, T.N.7
Siomi, M.C.8
Siomi, H.9
-
17
-
-
80052991624
-
3 End formation of PIWI-interacting RNAs in vitro
-
Kawaoka S, Izumi N, Katsuma S, Tomari Y (2011) 3 End formation of PIWI-interacting RNAs in vitro. Mol Cell 43: 1015-1022
-
(2011)
Mol Cell
, vol.43
, pp. 1015-1022
-
-
Kawaoka, S.1
Izumi, N.2
Katsuma, S.3
Tomari, Y.4
-
18
-
-
0142165224
-
Functional siRNAs and miRNAs exhibit strand bias
-
Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216
-
(2003)
Cell
, vol.115
, pp. 209-216
-
-
Khvorova, A.1
Reynolds, A.2
Jayasena, S.D.3
-
19
-
-
84856723932
-
The N domain of Argonaute drives duplex unwinding during RISC assembly
-
Kwak PB, Tomari Y (2012) The N domain of Argonaute drives duplex unwinding during RISC assembly. Nat Struct Mol Biol 19: 145-151
-
(2012)
Nat Struct Mol Biol
, vol.19
, pp. 145-151
-
-
Kwak, P.B.1
Tomari, Y.2
-
20
-
-
0035955361
-
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
-
Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862
-
(2001)
Science
, vol.294
, pp. 858-862
-
-
Lau, N.C.1
Lim, L.P.2
Weinstein, E.G.3
Bartel, D.P.4
-
21
-
-
70349641600
-
Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line
-
Lau NC, Robine N, Martin R, Chung W-J, Niki Y, Berezikov E, Lai EC (2009) Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res 19: 1776-1785
-
(2009)
Genome Res
, vol.19
, pp. 1776-1785
-
-
Lau, N.C.1
Robine, N.2
Martin, R.3
Chung, W.-J.4
Niki, Y.5
Berezikov, E.6
Lai, E.C.7
-
22
-
-
0016615696
-
Interrelation between glycosidic torsion, sugar pucker, and backbone conformation in 5-beta-nucleotides. A 1H and 31P fast Fourier transform nuclear magnetic resonance investigation of the conformation of 8-aza-5-beta-adenosine monophosphate and 8-aza-5-beta-guanosine monophosphate
-
Lee CH, Evans FE, Sarma RH (1975) Interrelation between glycosidic torsion, sugar pucker, and backbone conformation in 5-beta-nucleotides. A 1H and 31P fast Fourier transform nuclear magnetic resonance investigation of the conformation of 8-aza-5-beta-adenosine monophosphate and 8-aza-5-beta-guanosine monophosphate. J Biol Chem 250: 1290-1296
-
(1975)
J Biol Chem
, vol.250
, pp. 1290-1296
-
-
Lee, C.H.1
Evans, F.E.2
Sarma, R.H.3
-
23
-
-
77950929337
-
Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi
-
Lee H-C, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, Liu Y (2010) Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38: 803-814
-
(2010)
Mol Cell
, vol.38
, pp. 803-814
-
-
Lee, H.-C.1
Li, L.2
Gu, W.3
Xue, Z.4
Crosthwaite, S.K.5
Pertsemlidis, A.6
Lewis, Z.A.7
Freitag, M.8
Selker, E.U.9
Mello, C.C.10
Liu, Y.11
-
24
-
-
0346094457
-
Prediction of mammalian microRNA targets
-
Lewis BP, Shih I-H, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798
-
(2003)
Cell
, vol.115
, pp. 787-798
-
-
Lewis, B.P.1
Shih, I.-H.2
Jones-Rhoades, M.W.3
Bartel, D.P.4
Burge, C.B.5
-
25
-
-
70350005156
-
Binding and cleavage specificities of human Argonaute2
-
Lima WF, Wu H, Nichols JG, Sun H, Murray HM, Crooke ST (2009) Binding and cleavage specificities of human Argonaute2. J Biol Chem 284: 26017-26028
-
(2009)
J Biol Chem
, vol.284
, pp. 26017-26028
-
-
Lima, W.F.1
Wu, H.2
Nichols, J.G.3
Sun, H.4
Murray, H.M.5
Crooke, S.T.6
-
26
-
-
0345359925
-
Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain
-
Lingel A, Simon B, Izaurralde E, Sattler M (2003) Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426: 465-469
-
(2003)
Nature
, vol.426
, pp. 465-469
-
-
Lingel, A.1
Simon, B.2
Izaurralde, E.3
Sattler, M.4
-
28
-
-
2442679207
-
Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain
-
Ma J-B, Ye K, Patel DJ (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429: 318-322
-
(2004)
Nature
, vol.429
, pp. 318-322
-
-
Ma, J.-B.1
Ye, K.2
Patel, D.J.3
-
29
-
-
15844371219
-
Structural basis for 5-end-specific recognition of guide RNA by the A. fulgidus Piwi protein
-
Ma J-B, Yuan Y-R, Meister G, Pei Y, Tuschl T, Patel DJ (2005) Structural basis for 5-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434: 666-670
-
(2005)
Nature
, vol.434
, pp. 666-670
-
-
Ma, J.-B.1
Yuan, Y.-R.2
Meister, G.3
Pei, Y.4
Tuschl, T.5
Patel, D.J.6
-
30
-
-
34447508216
-
Phaser crystallographic software
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674
-
(2007)
J Appl Crystallogr
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
31
-
-
41349114789
-
Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5 terminal nucleotide
-
Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y (2008) Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5 terminal nucleotide. Cell 133: 116-127
-
(2008)
Cell
, vol.133
, pp. 116-127
-
-
Mi, S.1
Cai, T.2
Hu, Y.3
Chen, Y.4
Hodges, E.5
Ni, F.6
Wu, L.7
Li, S.8
Zhou, H.9
Long, C.10
Chen, S.11
Hannon, G.J.12
Qi, Y.13
-
32
-
-
41149158475
-
Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation
-
Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133: 128-141
-
(2008)
Cell
, vol.133
, pp. 128-141
-
-
Montgomery, T.A.1
Howell, M.D.2
Cuperus, J.T.3
Li, D.4
Hansen, J.E.5
Alexander, A.L.6
Chapman, E.J.7
Fahlgren, N.8
Allen, E.9
Carrington, J.C.10
-
33
-
-
0033638223
-
Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast
-
Mossessova E, Lima CD (2000) Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol Cell 5: 865-876
-
(2000)
Mol Cell
, vol.5
, pp. 865-876
-
-
Mossessova, E.1
Lima, C.D.2
-
34
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Carter Jr CW, Sweet RM (eds), Part A New York: Academic Press
-
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology, Volume 276: Macromolecular Crystallography, Carter Jr CW, Sweet RM (eds), Part A, pp 307-326. New York: Academic Press
-
(1997)
Methods in Enzymology, Volume 276: Macromolecular Crystallography
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
35
-
-
15844402005
-
Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex
-
Parker JS, Roe SM, Barford D (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434: 663-666
-
(2005)
Nature
, vol.434
, pp. 663-666
-
-
Parker, J.S.1
Roe, S.M.2
Barford, D.3
-
36
-
-
33845436047
-
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
-
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193-1207
-
(2006)
Cell
, vol.127
, pp. 1193-1207
-
-
Ruby, J.G.1
Jan, C.2
Player, C.3
Axtell, M.J.4
Lee, W.5
Nusbaum, C.6
Ge, H.7
Bartel, D.P.8
-
37
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208
-
(2003)
Cell
, vol.115
, pp. 199-208
-
-
Schwarz, D.S.1
Hutvágner, G.2
Du, T.3
Xu, Z.4
Aronin, N.5
Zamore, P.D.6
-
38
-
-
84856542174
-
A 5-uridine amplifies miRNA/miRNA asymmetry in Drosophila by promoting RNA-induced silencing complex formation
-
Seitz H, Tushir JS, Zamore PD (2011) A 5-uridine amplifies miRNA/miRNA asymmetry in Drosophila by promoting RNA-induced silencing complex formation. Silence 2: 4
-
(2011)
Silence
, vol.2
, pp. 4
-
-
Seitz, H.1
Tushir, J.S.2
Zamore, P.D.3
-
39
-
-
0345490960
-
The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes
-
Song J-J, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ, Joshua-Tor L (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol 10: 1026-1032
-
(2003)
Nat Struct Biol
, vol.10
, pp. 1026-1032
-
-
Song, J.-J.1
Liu, J.2
Tolia, N.H.3
Schneiderman, J.4
Smith, S.K.5
Martienssen, R.A.6
Hannon, G.J.7
Joshua-Tor, L.8
-
40
-
-
44349094874
-
The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins
-
Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol 49: 493-500
-
(2008)
Plant Cell Physiol
, vol.49
, pp. 493-500
-
-
Takeda, A.1
Iwasaki, S.2
Watanabe, T.3
Utsumi, M.4
Watanabe, Y.5
-
41
-
-
75649133887
-
Expanded RNA-binding activities of mammalian Argonaute 2
-
Tan G, Garchow B, Liu X, Yeung J, Morris J, Cuellar T, McManus MT, Kiriakidou M (2009) Expanded RNA-binding activities of mammalian Argonaute 2. Nucl Acids Res 37: 7533-7545
-
(2009)
Nucl Acids Res
, vol.37
, pp. 7533-7545
-
-
Tan, G.1
Garchow, B.2
Liu, X.3
Yeung, J.4
Morris, J.5
Cuellar, T.6
McManus, M.T.7
Kiriakidou, M.8
-
42
-
-
70350238350
-
The biogenesis and function of PIWI proteins and piRNAs: Progress and prospect
-
Thomson T, Lin H (2009) The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. Annu Rev Cell Dev Biol 25: 355-376
-
(2009)
Annu Rev Cell Dev Biol
, vol.25
, pp. 355-376
-
-
Thomson, T.1
Lin, H.2
-
43
-
-
70349961432
-
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes
-
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461: 754-761
-
(2009)
Nature
, vol.461
, pp. 754-761
-
-
Wang, Y.1
Juranek, S.2
Li, H.3
Sheng, G.4
Wardle, G.S.5
Tuschl, T.6
Patel, D.J.7
-
44
-
-
23144438396
-
Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage
-
Yuan Y-R, Pei Y, Ma J-B, Kuryavyi V, Zhadina M, Meister G, Chen H-Y, Dauter Z, Tuschl T, Patel DJ (2005) Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell 19: 405-419
-
(2005)
Mol Cell
, vol.19
, pp. 405-419
-
-
Yuan, Y.-R.1
Pei, Y.2
Ma, J.-B.3
Kuryavyi, V.4
Zhadina, M.5
Meister, G.6
Chen, H.-Y.7
Dauter, Z.8
Tuschl, T.9
Patel, D.J.10
|