-
1
-
-
0024977414
-
Five intermediate complexes in transcription initiation by RNA polymerase II
-
Buratowski, S., Hahn, S., Guarente, L. & Sharp, P. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56, 549-561 (1989).
-
(1989)
Cell
, vol.56
, pp. 549-561
-
-
Buratowski, S.1
Hahn, S.2
Guarente, L.3
Sharp, P.4
-
2
-
-
81255210794
-
Transcriptional regulation in Saccharomyces cerevisiae: Transcription factor regulation and function, mechanismsof initiation, and roles of activators and coactivators
-
Hahn, S. & Young, E. T. Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanismsof initiation, and roles of activators and coactivators. Genetics 189, 705-736 (2011).
-
(2011)
Genetics
, vol.189
, pp. 705-736
-
-
Hahn, S.1
Young, E.T.2
-
3
-
-
70450171352
-
RNA polymerase II-TFIIB structure and mechanism of transcription initiation
-
Kostrewa, D. et al. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462, 323-330 (2009).
-
(2009)
Nature
, vol.462
, pp. 323-330
-
-
Kostrewa, D.1
-
4
-
-
74249102477
-
Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism
-
Liu, X., Bushnell, D., Wang, D., Calero, G. & Kornberg, R. D. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327, 206-209 (2010).
-
(2010)
Science
, vol.327
, pp. 206-209
-
-
Liu, X.1
Bushnell, D.2
Wang, D.3
Calero, G.4
Kornberg, R.D.5
-
5
-
-
84864662191
-
Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening
-
Grünberg, S., Warfield, L. & Hahn, S. Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nature Struct. Mol. Biol. 19, 788-796 (2012).
-
(2012)
Nature Struct. Mol. Biol.
, vol.19
, pp. 788-796
-
-
Grünberg, S.1
Warfield, L.2
Hahn, S.3
-
6
-
-
84872614213
-
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex
-
Sainsbury, S., Niesser, J. & Cramer, P. Structure and function of the initially transcribing RNA polymerase II-TFIIB complex. Nature 493, 437-440 (2013).
-
(2013)
Nature
, vol.493
, pp. 437-440
-
-
Sainsbury, S.1
Niesser, J.2
Cramer, P.3
-
7
-
-
84875613843
-
Structural visualization of key steps in human transcription initiation
-
He, Y., Fang, J., Taatjes, D. & Nogales, E. Structural visualization of key steps in human transcription initiation. Nature 495, 481-486 (2013).
-
(2013)
Nature
, vol.495
, pp. 481-486
-
-
He, Y.1
Fang, J.2
Taatjes, D.3
Nogales, E.4
-
8
-
-
84884516365
-
Architecture of anRNApolymerase II transcriptionpre-initiation complex
-
Murakami, K. et al. Architecture of anRNApolymerase II transcriptionpre-initiation complex. Science 342, 1238724 (2013).
-
(2013)
Science
, vol.342
, pp. 1238724
-
-
Murakami, K.1
-
9
-
-
84904346675
-
Conserved architecture of the core RNA polymerase II initation complex
-
Mü hlbacher, W. et al. Conserved architecture of the core RNA polymerase II initation complex. Nature Commun. 5, 4310 (2014).
-
(2014)
Nature Commun.
, vol.5
, pp. 4310
-
-
Mü Hlbacher, W.1
-
10
-
-
80455164640
-
Origins and activity of the Mediator complex
-
Conaway, R. C. & Conaway, J. Origins and activity of the Mediator complex. Semin. Cell Dev. Biol. 22, 729-734 (2011).
-
(2011)
Semin. Cell Dev. Biol.
, vol.22
, pp. 729-734
-
-
Conaway, R.C.1
Conaway, J.2
-
11
-
-
34347273423
-
Hyperphosphorylation of the C-terminal repeat domain of RNA polymerase II facilitates dissociation of its complex with mediator
-
Max, T., Søgaard, M. & Svejstrup, J. Q. Hyperphosphorylation of the C-terminal repeat domain of RNA polymerase II facilitates dissociation of its complex with mediator. J. Biol. Chem. 282, 14113-14120 (2007).
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 14113-14120
-
-
Max, T.1
Søgaard, M.2
Svejstrup, J.Q.3
-
12
-
-
84861963339
-
A structural perspective on Mediator function
-
Larivière, L., Seizl, M. & Cramer, P. A structural perspective on Mediator function. Curr. Opin. Cell Biol. 24, 305-313 (2012).
-
(2012)
Curr. Opin. Cell Biol.
, vol.24
, pp. 305-313
-
-
Larivière, L.1
Seizl, M.2
Cramer, P.3
-
13
-
-
79960434142
-
Architecture of the Mediator head module
-
Imasaki, T. et al. Architecture of the Mediator head module. Nature 475, 240-243 (2011).
-
(2011)
Nature
, vol.475
, pp. 240-243
-
-
Imasaki, T.1
-
14
-
-
84871456902
-
Structure of the Mediator head module
-
Larivière, L. et al. Structure of the Mediator head module. Nature 492, 448-451 (2012).
-
(2012)
Nature
, vol.492
, pp. 448-451
-
-
Larivière, L.1
-
15
-
-
84868094446
-
Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II
-
Robinson, P. J., Bushnell, D., Trnka, M., Burlingame, A. & Kornberg, R. Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc. Natl Acad. Sci. USA 109, 17931-17935 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 17931-17935
-
-
Robinson, P.J.1
Bushnell, D.2
Trnka, M.3
Burlingame, A.4
Kornberg, R.5
-
16
-
-
84903816704
-
Redefining the modular organization of the core Mediator complex
-
Wang, X. et al. Redefining the modular organization of the core Mediator complex. Cell Res. 24, 796-808 (2014).
-
(2014)
Cell Res.
, vol.24
, pp. 796-808
-
-
Wang, X.1
-
17
-
-
84902186552
-
Subunit architecture and functional modular rearrangements of the transcriptional mediator complex
-
Tsai, K.-L. et al. Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Cell 157, 1430-1444 (2014).
-
(2014)
Cell
, vol.157
, pp. 1430-1444
-
-
Tsai, K.-L.1
-
18
-
-
0038832859
-
Conserved structures ofMediator and RNA polymerase II holoenzyme
-
Asturias, F. J., Jiang, Y. W., Myers, L. C., Gustafson, C. M. Kornberg, R. D.Conserved structures ofMediator andRNApolymerase IIholoenzyme. Science 283, 985-987 (1999).
-
(1999)
Science
, vol.283
, pp. 985-987
-
-
Asturias, F.J.1
Jiang, Y.W.2
Myers, L.C.3
Gustafson, M.4
Kornberg, R.D.5
-
19
-
-
0036671095
-
Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction
-
Davis, J. A., Takagi, Y., Kornberg, R. & Asturias, F. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell 10, 409-415 (2002).
-
(2002)
Mol. Cell
, vol.10
, pp. 409-415
-
-
Davis, J.A.1
Takagi, Y.2
Kornberg, R.3
Asturias, F.4
-
20
-
-
33750481873
-
The cyclin-dependent kinase 8module sterically blocksMediator interactions with RNA polymerase II
-
Elmlund, H. et al. The cyclin-dependent kinase 8module sterically blocksMediator interactions with RNA polymerase II. Proc. Natl Acad. Sci. USA 103, 15788-15793 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 15788-15793
-
-
Elmlund, H.1
-
21
-
-
79953713243
-
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly
-
Bernecky, C., Grob, P., Ebmeier, C., Nogales, E. & Taatjes, D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biol. 9, e1000603 (2011).
-
(2011)
PLoS Biol.
, vol.9
, pp. e1000603
-
-
Bernecky, C.1
Grob, P.2
Ebmeier, C.3
Nogales, E.4
Taatjes, D.5
-
22
-
-
85027942059
-
A conserved Mediator-CDK8 kinase module association regulates Mediator-RNA polymerase II interaction
-
Tsai, K.-L. et al. A conserved Mediator-CDK8 kinase module association regulates Mediator-RNA polymerase II interaction. Nature Struct. Mol. Biol. 20, 611-619 (2013).
-
(2013)
Nature Struct. Mol. Biol.
, vol.20
, pp. 611-619
-
-
Tsai, K.-L.1
-
23
-
-
0035831475
-
Yeast nuclear extract contains twomajor forms of RNA polymerase II mediator complexes
-
Liu, Y., Ranish, J., Aebersold, R.& Hahn, S. Yeast nuclear extract contains twomajor forms of RNA polymerase II mediator complexes. J. Biol. Chem. 276, 7169-7175 (2001).
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 7169-7175
-
-
Liu, Y.1
Ranish, J.2
Aebersold, R.3
Hahn, S.4
-
24
-
-
84923319299
-
Reconstitution of active humancoreMediator complex reveals a critical role of the MED14 subunit
-
Cevher, M. A. et al. Reconstitution of active humancoreMediator complex reveals a critical role of the MED14 subunit. Nature Struct. Mol. Biol. 21, 1028-1034 (2014).
-
(2014)
Nature Struct. Mol. Biol.
, vol.21
, pp. 1028-1034
-
-
Cevher, M.A.1
-
25
-
-
84890062562
-
Model of the Mediator middle module based on protein crosslinking
-
Larivière, L. et al. Model of the Mediator middle module based on protein crosslinking. Nucleic Acids Res. 41, 9266-9273 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 9266-9273
-
-
Larivière, L.1
-
26
-
-
0001603028
-
An activator binding module of yeast RNA polymerase II holoenzyme
-
Lee, Y. C., Park, J., Min, S., Han, S. & Kim, Y. An activator binding module of yeast RNA polymerase II holoenzyme. Mol. Cell. Biol. 19, 2967-2976 (1999).
-
(1999)
Mol. Cell. Biol.
, vol.19
, pp. 2967-2976
-
-
Lee, Y.C.1
Park, J.2
Min, S.3
Han, S.4
Kim, Y.5
-
27
-
-
47249134314
-
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex
-
Bourbon, H.-M. Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res. 36, 3993-4008 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 3993-4008
-
-
Bourbon, H.-M.1
-
28
-
-
77149124577
-
Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex
-
Eichner, J., Chen, H.-T., Warfield, L. & Hahn, S. Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. EMBO J. 29, 706-716 (2010).
-
(2010)
EMBO J.
, vol.29
, pp. 706-716
-
-
Eichner, J.1
Chen, H.-T.2
Warfield, L.3
Hahn, S.4
-
29
-
-
84869862306
-
Structural basis of transcription initiation
-
Zhang, Y. et al. Structural basis of transcription initiation. Science 338, 1076-1080 (2012).
-
(2012)
Science
, vol.338
, pp. 1076-1080
-
-
Zhang, Y.1
-
30
-
-
77149146167
-
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry
-
Chen, Z. A. et al. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 29, 717-726 (2010).
-
(2010)
EMBO J.
, vol.29
, pp. 717-726
-
-
Chen, Z.A.1
-
31
-
-
84856781205
-
Architecture of the yeast RNA polymerase II open complex and regulation of activity by TFIIF
-
Fishburn, J. & Hahn, S. Architecture of the yeast RNA polymerase II open complex and regulation of activity by TFIIF. Mol. Cell. Biol. 32, 12-25 (2012).
-
(2012)
Mol. Cell. Biol.
, vol.32
, pp. 12-25
-
-
Fishburn, J.1
Hahn, S.2
-
32
-
-
33749514827
-
Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20
-
Larivière, L. et al. Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nature Struct. Mol. Biol. 13, 895-901 (2006).
-
(2006)
Nature Struct. Mol. Biol.
, vol.13
, pp. 895-901
-
-
Larivière, L.1
-
33
-
-
58149351376
-
Identification, structure, and functional requirement of the Mediator submodule Med7N/31
-
Koschubs, T. et al. Identification, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J. 28, 69-80 (2009).
-
(2009)
EMBO J.
, vol.28
, pp. 69-80
-
-
Koschubs, T.1
-
34
-
-
0025962218
-
Two dissociable subunits of yeast RNApolymerase II stimulate the initiation of transcription at a promoter in vitro
-
Edwards, A. M., Kane, C. M., Young, R. A. & Kornberg, R. D.Two dissociable subunits of yeast RNApolymerase II stimulate the initiation of transcription at a promoter in vitro. J. Biol. Chem. 266, 71-75 (1991).
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 71-75
-
-
Edwards, A.M.1
Kane, C.M.2
Young, R.A.3
Kornberg, R.D.4
-
35
-
-
33744948144
-
Human Mediator enhances basal transcription by facilitating recruitment of transcription factor IIB during preinitiation complex assembly
-
Baek, H. J., Kang, Y.& Roeder, R. Human Mediator enhances basal transcription by facilitating recruitment of transcription factor IIB during preinitiation complex assembly. J. Biol. Chem. 281, 15172-15181 (2006).
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 15172-15181
-
-
Baek, H.J.1
Kang, Y.2
Roeder, R.3
-
36
-
-
0032900980
-
Intermediates in formationandactivity of the RNA polymerase II preinitiation complex: Holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB
-
Ranish, J. A., Yudkovsky, N. & Hahn, S. Intermediates in formationandactivity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev. 13, 49-63 (1999).
-
(1999)
Genes Dev.
, vol.13
, pp. 49-63
-
-
Ranish, J.A.1
Yudkovsky, N.2
Hahn, S.3
-
37
-
-
0027253864
-
A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast
-
Thompson, C. M., Koleske, A., Chao, D. & Young, R. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell 73, 1361-1375 (1993).
-
(1993)
Cell
, vol.73
, pp. 1361-1375
-
-
Thompson, C.M.1
Koleske, A.2
Chao, D.3
Young, R.4
-
38
-
-
79952803747
-
Direct interaction of RNA polymerase II and mediator required for transcription in vivo
-
Soutourina, J., Wydau, S., Ambroise, Y., Boschiero, C. & Werner, M. Direct interaction of RNA polymerase II and mediator required for transcription in vivo. Science 331, 1451-1454 (2011).
-
(2011)
Science
, vol.331
, pp. 1451-1454
-
-
Soutourina, J.1
Wydau, S.2
Ambroise, Y.3
Boschiero, C.4
Werner, M.5
-
39
-
-
0024354605
-
Intragenic and extragenic suppressors ofmutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II
-
Nonet, M. L.& Young, R. Intragenic and extragenic suppressors ofmutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 123, 715-724 (1989).
-
(1989)
Genetics
, vol.123
, pp. 715-724
-
-
Nonet, M.L.1
Young, R.2
-
40
-
-
14844290215
-
Structures of complete RNA polymerase II and its subcomplex Rpb4/7
-
Armache, K. J., Mitterweger, S., Meinhart, A. & Cramer, P. Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J. Biol. Chem. 280, 7131-7134 (2005).
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 7131-7134
-
-
Armache, K.J.1
Mitterweger, S.2
Meinhart, A.3
Cramer, P.4
-
41
-
-
33748753071
-
The classical srb4-138 mutant allele causes dissociation of yeast Mediator
-
Linder, T., Zhu, X., Baraznenok, V. & Gustafsson, C. The classical srb4-138 mutant allele causes dissociation of yeast Mediator. Biochem. Biophys. Res. Commun. 349, 948-953 (2006).
-
(2006)
Biochem. Biophys. Res. Commun.
, vol.349
, pp. 948-953
-
-
Linder, T.1
Zhu, X.2
Baraznenok, V.3
Gustafsson, C.4
-
42
-
-
33644852483
-
Mediator as a general transcription factor
-
Takagi, Y. & Kornberg, R. D.Mediator as a general transcription factor. J. Biol. Chem. 281, 80-89 (2006).
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 80-89
-
-
Takagi, Y.1
Kornberg, R.D.2
-
43
-
-
33746408090
-
Head module control of mediator interactions
-
Takagi, Y. et al. Head module control of mediator interactions. Mol. Cell 23, 355-364 (2006).
-
(2006)
Mol. Cell
, vol.23
, pp. 355-364
-
-
Takagi, Y.1
-
44
-
-
84863540819
-
Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
-
Sun, M. et al. Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res. 22, 1350-1359 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1350-1359
-
-
Sun, M.1
-
45
-
-
84903471633
-
Rpb4 subunit functions mainly in mRNA synthesis by RNA polymerase II
-
Schulz, D., Pirkl, N., Lehmann, E. & Cramer, P. Rpb4 subunit functions mainly in mRNA synthesis by RNA polymerase II. J. Biol. Chem. 289, 17446-17452 (2014).
-
(2014)
J. Biol. Chem.
, vol.289
, pp. 17446-17452
-
-
Schulz, D.1
Pirkl, N.2
Lehmann, E.3
Cramer, P.4
-
46
-
-
84886948058
-
RNA polymerase i structure and transcription regulation
-
Engel, C., Sainsbury, S., Cheung, A., Kostrewa, D. & Cramer, P. RNA polymerase I structure and transcription regulation. Nature 502, 650-655 (2013).
-
(2013)
Nature
, vol.502
, pp. 650-655
-
-
Engel, C.1
Sainsbury, S.2
Cheung, A.3
Kostrewa, D.4
Cramer, P.5
-
47
-
-
0035827346
-
Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
-
Cramer, P., Bushnell, D. & Kornberg, R. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863-1876 (2001).
-
(2001)
Science
, vol.292
, pp. 1863-1876
-
-
Cramer, P.1
Bushnell, D.2
Kornberg, R.3
-
48
-
-
0043244876
-
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
-
Kettenberger, H., Armache, K.-J. & Cramer, P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114, 347-357 (2003).
-
(2003)
Cell
, vol.114
, pp. 347-357
-
-
Kettenberger, H.1
Armache, K.-J.2
Cramer, P.3
-
49
-
-
84871700533
-
Mediator-regulated transcription through the 11 nucleosome
-
Nock, A., Ascano, J., Barrero, M. & Malik, S. Mediator-regulated transcription through the 11 nucleosome. Mol. Cell 48, 837-848 (2012).
-
(2012)
Mol. Cell
, vol.48
, pp. 837-848
-
-
Nock, A.1
Ascano, J.2
Barrero, M.3
Malik, S.4
-
50
-
-
48349095490
-
Mediator-dependent recruitment of TFIIHmodules in preinitiation complex
-
Esnault, C. et al. Mediator-dependent recruitment of TFIIHmodules in preinitiation complex. Mol. Cell 31, 337-346 (2008).
-
(2008)
Mol. Cell
, vol.31
, pp. 337-346
-
-
Esnault, C.1
-
51
-
-
0028826925
-
Yeast global transcriptional regulators Sin4 andRgr1 are components of mediator complex/RNA polymerase II holoenzyme
-
Li, Y. et al. Yeast global transcriptional regulators Sin4 andRgr1 are components of mediator complex/RNA polymerase II holoenzyme. Proc. Natl Acad. Sci. USA 92, 10864-10868 (1995).
-
(1995)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 10864-10868
-
-
Li, Y.1
-
52
-
-
24044470632
-
A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer
-
Baumli, S., Hoeppner, S. & Cramer, P. A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J. Biol. Chem. 280, 18171-18178 (2005).
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 18171-18178
-
-
Baumli, S.1
Hoeppner, S.2
Cramer, P.3
-
53
-
-
80051729454
-
Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcriptioninitiationcomplex stabilization
-
Seizl, M., Larivière, L., Pfaffeneder, T., Wenzeck, L. & Cramer, P. Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcriptioninitiationcomplex stabilization.Nucleic Acids Res. 39, 6291-6304 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6291-6304
-
-
Seizl, M.1
Larivière, L.2
Pfaffeneder, T.3
Wenzeck, L.4
Cramer, P.5
-
54
-
-
0842304212
-
RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: The major stable Pol II complexes and their activity in transcription initiation and reinitiation
-
Rani, P. G., Ranish, J. & Hahn, S.RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation. Mol. Cell. Biol. 24, 1709-1720 (2004).
-
(2004)
Mol. Cell. Biol.
, vol.24
, pp. 1709-1720
-
-
Rani, P.G.1
Ranish, J.2
Hahn, S.3
-
55
-
-
67449116330
-
Structural basis of transcription: Mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
-
Sydow, J. F. et al. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol. Cell 34, 710-721 (2009).
-
(2009)
Mol. Cell
, vol.34
, pp. 710-721
-
-
Sydow, J.F.1
-
56
-
-
0027504913
-
Crystal structure of a yeast TBP/TATAbox complex
-
Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. Crystal structure of a yeast TBP/TATAbox complex. Nature 365, 512-520 (1993).
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Geiger, J.H.2
Hahn, S.3
Sigler, P.B.4
-
57
-
-
34547683177
-
The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex
-
Chen, H.-T., Warfield, L. & Hahn, S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nature Struct. Mol. Biol. 14, 696-703 (2007).
-
(2007)
Nature Struct. Mol. Biol.
, vol.14
, pp. 696-703
-
-
Chen, H.-T.1
Warfield, L.2
Hahn, S.3
-
58
-
-
0346515712
-
Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae
-
Kireeva, M. L., Lubkowska, L., Komissarova, N. & Kashlev, M. Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae. Methods Enzymol. 370, 138-155 (2003).
-
(2003)
Methods Enzymol.
, vol.370
, pp. 138-155
-
-
Kireeva, M.L.1
Lubkowska, L.2
Komissarova, N.3
Kashlev, M.4
-
59
-
-
77955381399
-
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics
-
Leitner, A. et al. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol. Cell. Proteomics 9, 1634-1649 (2010).
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 1634-1649
-
-
Leitner, A.1
-
60
-
-
84866095385
-
Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry
-
Herzog, F. et al. Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science 337, 1348-1352 (2012).
-
(2012)
Science
, vol.337
, pp. 1348-1352
-
-
Herzog, F.1
-
61
-
-
84891714984
-
Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline
-
Leitner, A., Walzthoeni, T. & Aebersold, R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nature Protocols 9, 120-137 (2014).
-
(2014)
Nature Protocols
, vol.9
, pp. 120-137
-
-
Leitner, A.1
Walzthoeni, T.2
Aebersold, R.3
-
62
-
-
77249179311
-
ICC-CLASS: Isotopically-coded cleavable crosslinking analysis software suite
-
Petrotchenko, E. V. & Borchers, C. ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. BMC Bioinformatics 11, 64 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 64
-
-
Petrotchenko, E.V.1
Borchers, C.2
-
63
-
-
25644458666
-
Automated electron microscope tomography using robust prediction of specimen movements
-
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36-51 (2005).
-
(2005)
J. Struct. Biol.
, vol.152
, pp. 36-51
-
-
Mastronarde, D.N.1
-
64
-
-
79960898027
-
Computer controlled cryo-electron microscopy-TOM2 a software package for high-throughput applications
-
Korinek, A., Beck, F., Baumeister, W., Nickell, S.& Plitzko, J. M. Computer controlled cryo-electron microscopy-TOM2 a software package for high-throughput applications. J. Struct. Biol. 175, 394-405 (2011).
-
(2011)
J. Struct. Biol.
, vol.175
, pp. 394-405
-
-
Korinek, A.1
Beck, F.2
Baumeister, W.3
Nickell, S.4
Plitzko, J.M.5
-
65
-
-
84880848354
-
Electron counting and beam-induced motion correction enable nearatomic-resolution single-particle cryo-EM
-
Li, X. et al. Electron counting and beam-induced motion correction enable nearatomic-resolution single-particle cryo-EM. Nature Methods 10, 584-590 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 584-590
-
-
Li, X.1
-
66
-
-
84868496402
-
Unraveling the structure ofmembrane proteins in situ by transfer function corrected cryo-electron tomography
-
Eibauer, M. et al. Unraveling the structure ofmembrane proteins in situ by transfer function corrected cryo-electron tomography. J. Struct. Biol.180, 488-496 (2012).
-
(2012)
J. Struct. Biol.
, vol.180
, pp. 488-496
-
-
Eibauer, M.1
-
67
-
-
33845332754
-
EMAN2: An extensible image processing suite for electron microscopy
-
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38-46 (2007).
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 38-46
-
-
Tang, G.1
-
68
-
-
84878285959
-
Fast and accurate referencefree alignment of subtomograms
-
Chen, Y., Pfeffer, S., Hrabe, T., Schuller, J. & Förster, F. Fast and accurate referencefree alignment of subtomograms. J. Struct. Biol. 182, 235-245 (2013).
-
(2013)
J. Struct. Biol.
, vol.182
, pp. 235-245
-
-
Chen, Y.1
Pfeffer, S.2
Hrabe, T.3
Schuller, J.4
Förster, F.5
-
69
-
-
84860584901
-
PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis
-
Hrabe, T. et al. PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J. Struct. Biol. 178, 177-188 (2012).
-
(2012)
J. Struct. Biol.
, vol.178
, pp. 177-188
-
-
Hrabe, T.1
-
70
-
-
84868444740
-
RELION: Implementation of a Bayesian approach to cryo-EM structure determination
-
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519-530 (2012).
-
(2012)
J. Struct. Biol.
, vol.180
, pp. 519-530
-
-
Scheres, S.H.1
-
71
-
-
58049204808
-
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs
-
Shaikh, T. R. et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols 3, 1941-1974 (2008).
-
(2008)
Nature Protocols
, vol.3
, pp. 1941-1974
-
-
Shaikh, T.R.1
-
72
-
-
0038441501
-
Accurate determinationof local defocus and specimen tilt in electron microscopy
-
Mindell, J. A. & Grigorieff, N. Accurate determinationof local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334-347 (2003).
-
(2003)
J. Struct. Biol.
, vol.142
, pp. 334-347
-
-
Mindell, J.A.1
Grigorieff, N.2
-
73
-
-
84887242753
-
One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions
-
Cardone, G., Heymann, J. B. & Steven, A. C. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184, 226-236 (2013).
-
(2013)
J. Struct. Biol.
, vol.184
, pp. 226-236
-
-
Cardone, G.1
Heymann, J.B.2
Steven, A.C.3
-
74
-
-
33644847296
-
Estimation of variance in singleparticle reconstruction using the bootstrap technique
-
Penczek, P. A., Yang, C., Frank, J. & Spahn, C. M. T. Estimation of variance in singleparticle reconstruction using the bootstrap technique. J. Struct. Biol.154,168-183 (2006).
-
(2006)
J. Struct. Biol.
, vol.154
, pp. 168-183
-
-
Penczek, P.A.1
Yang, C.2
Frank, J.3
Spahn, C.M.T.4
-
75
-
-
2042540051
-
Gridding-based direct Fourier inversion of the three-dimensional ray transform
-
Penczek, P. A., Renka, R. & Schomberg, H. Gridding-based direct Fourier inversion of the three-dimensional ray transform. J. Opt. Soc. Am. A 21, 499-509 (2004).
-
(2004)
J. Opt. Soc. Am. A
, vol.21
, pp. 499-509
-
-
Penczek, P.A.1
Renka, R.2
Schomberg, H.3
-
76
-
-
77955358961
-
Using Situs for the integration ofmulti-resolution structures
-
Wriggers, W. Using Situs for the integration ofmulti-resolution structures. Biophys. Rev. 2, 21-27 (2010).
-
(2010)
Biophys. Rev.
, vol.2
, pp. 21-27
-
-
Wriggers, W.1
-
77
-
-
4444221565
-
UCSF Chimera- A visualization system for exploratory research and analysis
-
Pettersen, E. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.1
-
78
-
-
82455199223
-
Structural basis of initial RNA polymerase II transcription
-
Cheung, A. C. M., Sainsbury, S. & Cramer, P. Structural basis of initial RNA polymerase II transcription. EMBO J. 30, 4755-4763 (2011).
-
(2011)
EMBO J.
, vol.30
, pp. 4755-4763
-
-
Cheung, A.C.M.1
Sainsbury, S.2
Cramer, P.3
-
79
-
-
13244281317
-
Coot: Model-building tools for molecular graphics
-
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
-
(2004)
Acta Crystallogr. D
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
80
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802 (2005).
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
-
81
-
-
84986512474
-
CHARMM: A programformacromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R. et al.CHARMM: a programformacromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187-217 (1983).
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
-
82
-
-
43749107283
-
Comparative protein structure modeling using Modeller
-
Eswar, N. et al. Comparative protein structure modeling using Modeller. Curr. Protocols Bioinf. 5, 5.6.1-5.6.30 (2006).
-
(2006)
Curr. Protocols Bioinf.
, vol.5
, pp. 561-5630
-
-
Eswar, N.1
-
83
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
-
(2010)
Acta Crystallogr. D
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
-
84
-
-
84885359411
-
Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels
-
Sun, M. et al. Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels. Mol. Cell 52, 52-62 (2013).
-
(2013)
Mol. Cell
, vol.52
, pp. 52-62
-
-
Sun, M.1
-
85
-
-
64049097892
-
Mediator structural conservation and implications for the regulation mechanism
-
Cai, G., Imasaki, T., Takagi, Y. & Asturias, F. J. Mediator structural conservation and implications for the regulation mechanism. Structure 17, 559-567 (2009).
-
(2009)
Structure
, vol.17
, pp. 559-567
-
-
Cai, G.1
Imasaki, T.2
Takagi, Y.3
Asturias, F.J.4
-
86
-
-
84861082442
-
Interaction of the mediator head module with RNA polymerase II
-
Cai, G. et al. Interaction of the mediator head module with RNA polymerase II. Structure 20, 899-910 (2012).
-
(2012)
Structure
, vol.20
, pp. 899-910
-
-
Cai, G.1
-
87
-
-
77953713807
-
Preparation and topology of the Mediator middle module
-
Koschubs, T. et al. Preparation and topology of the Mediator middle module. Nucleic Acids Res. 38, 3186-3195 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 3186-3195
-
-
Koschubs, T.1
|