Publications

Journal Article (309)

1.
Journal Article
Cramer, P.: Good reasons for structural biology. Nature Structural & Molecular Biology (2024)
2.
Journal Article
Frieg, B.; Han, M.; Giller, K.; Dienemann, C.; Riedel, D.; Becker, S.; Andreas, L. B.; Griesinger, C.; Schröder, G. F.: Cryo-EM structures of lipidic fibrils of amyloid-β (1-40). Nature Communications 15, 1297 (2024)
3.
Journal Article
Düring, J.; Wolter, M.; Toplak, J. J.; Torres, C.; Dybkov, O.; Fokkens, T. J.; Bohnsack, K. E.; Urlaub, H.; Steinchen, W.; Dienemann, C. et al.; Lorenz, S.: Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1. Nature Structural & Molecular Biology 31, pp. 364 - 377 (2024)
4.
Journal Article
Kokic, G.; Yakoub, G.; van den Heuvel, D.; Wondergem, A. P.; van der Meer, P. J.; van der Weegen, Y.; Chernev, A.; Fianu, I.; Fokkens, T. J.; Lorenz, S. et al.; Urlaub, H.; Cramer, P.; Luijsterburg, M. S.: Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair. Nature Structural & Molecular Biology (2024)
5.
Journal Article
Oberbeckmann, E.; Quililan, K.; Cramer, P.; Oudelaar, A. M.: In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization. Nature Genetics (2024)
6.
Journal Article
Chaban, A.; Minakhin, L.; Goldobina, E.; Bae, B.; Hao, Y.; Borukhov, S.; Putzeys, L.; Boon, M.; Kabinger, F.; Lavigne, R. et al.; Makarova, K.S.; Koonin, E.V.; Nair, S.K.; Tagami, S.; Severinov, K.; Sokolova, M. L.: Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail. Nature Communications 15, 317 (2024)
7.
Journal Article
MacCarthy, C. M.; Wu, G.; Malik, V.; Menuchin-Lasowski, Y.; Velychko, T.; Keshet, G.; Fan, R.; Bedzhov, I.; Church, G. M.; Jauch, R. et al.; Cojocaru, V.; Schoeler, H. R.; Velychko, S.: Highly cooperative chimeric super-SOX induces naive pluripotency across species. Cell Stem Cell 31 (1), e9, pp. 127 - 147 (2024)
8.
Journal Article
Chen, Y.; Cramer, P.: RNA polymerase II elongation factors use conserved regulatory mechanisms. Current Opinion in Structural Biology 84, 102766 (2024)
9.
Journal Article
Sun, Y.; Wiese, M.; Hmadi, R.; Karayol, R.; Seyfferth, J.; Martinez Greene, J.A.; Erdogdu, N.U.; Deboutte, W.; Arrigoni, L.; Holz, H. et al.; Renschler, G.; Hirsch, N.; Foertsch, A.; Basilicata, M.F.; Stehle, T.; Shvedunova, M.; Bella, C.; Pessoa Rodrigues, C.; Schwalb, B.; Cramer, P.; Manke, T.; Akhtar, A.: MSL2 ensures biallelic gene expression in mammals. Nature 624 (7990), pp. 173 - 181 (2023)
10.
Journal Article
Chen, Y.; Kokic, G.; Dienemann, C.; Dybkov, O.; Urlaub, H.; Cramer, P.: Structure of the transcribing RNA polymerase II–Elongin complex. Nature Structural & Molecular Biology 30, pp. 1925 - 1935 (2023)
11.
Journal Article
Palau, A.; Segerberg, F.; Lidschreiber, M.; Lidschreiber, K.; Naughton, A.J.; Needhamsen, M.; Jung, L.A.; Jagodic, M.; Cramer, P.; Lehmann, S. et al.; Carlsten, M.; Lennartsson, A.: Perturbed epigenetic transcriptional regulation in AML with IDH mutations causes increased susceptibility to NK cells. Leukemia 37, pp. 1830 - 1841 (2023)
12.
Journal Article
Garg, G.; Dienemann, C.; Farnung, L.; Schwarz, J.; Linden, A.; Urlaub, H.; Cramer, P.: Structural insights into human co-transcriptional capping. Molecular Cell 83 (14), pp. 2464 - 2477.e5 (2023)
13.
Journal Article
Rouvière, J. O.; Salerno-Kochan, A.; Lykke-Andersen, S.; Garland, W.; Dou, Y.; Rathore, O.; Molska, E. Š.; Wu, G.; Schmid, M.; Bugai, A. et al.; Jakobsen, L.; Zumer, K.; Cramer, P.; Andersen, J. S.; Conti, E.; Jensen, T. H.: ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts. Molecular Cell 83 (13), pp. 2240 - 2257 (2023)
14.
Journal Article
Ramasamy, S.; Aljahani, A.; Karpinska, M. A.; Cao, N. T. B.; Velychko, T.; Cruz, J. N.; Lidschreiber, M.; Oudelaar, A. M.: The Mediator complex regulates enhancer-promoter interactions. Nature Structural and Molecular Biology 30, pp. 991 - 1000 (2023)
15.
Journal Article
Abril-Garrido, J.; Dienemann, C.; Grabbe, F.; Velychko, T.; Lidschreiber, M.; Wang, H.; Cramer, P.: Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Molecular Cell 83 (11), pp. 1798 - 1809.e7 (2023)
16.
Journal Article
Schmitzová, J.; Cretu, C.; Dienemann, C.; Urlaub, H.; Pena, V.: Structural basis of catalytic activation in human splicing. Nature 617, pp. 842 - 850 (2023)
17.
Journal Article
Rengachari, S.; Schilbach, S.; Cramer, P.: Mediator structure and function in transcription initiation. Biological Chemistry, aop (2023)
18.
Journal Article
Schilbach, S.; Wang, H.; Dienemann, C.; Cramer, P.: Yeast PIC-mediator structure with RNA polymerase II C-terminal domain. Proceedings of the National Academy of Sciences of the United States of America 120 (15), e2220542120 (2023)
19.
Journal Article
Dybkov, O.; Preußner, M.; El Ayoubi, L.; Feng, V.-Y.; Harnisch, C.; Merz, K.; Leupold, P.; Yudichev, P.; Agafonov, D. E.; Will, C. L. et al.; Girard, C.; Dienemann, C.; Urlaub, H.; Kastner, B.; Heyd, F.; Lührmann, R.: Regulation of 3′ splice site selection after step 1 of splicing by spliceosomal C* proteins. Science Advances 9 (9), eadf178 (2023)
20.
Journal Article
Wang, H.; Schilbach, S.; Ninov, M.; Urlaub, H.; Cramer, P.: Structures of transcription preinitiation complex engaged with the +1 nucleosome. Nature Structural and Molecular Biology 30, pp. 226 - 232 (2023)
21.
Journal Article
Dienemann, C.: Towards automating single-particle cryo-EM data acquisition. IUCRJ 10 (Part 1), pp. 4 - 5 (2023)
22.
Journal Article
Flores-Solis, D.; Lushpinskaia, I.P.; Polyansky, A.A.; Changiarath, A.; Boehning, M.; Mirkovic, M.; Walshe, J.; Pietrek, L.M.; Cramer, P.; Stelzl, L.S. et al.; Zagrovic, B.; Zweckstetter, M.: Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nature Communications 14 (1), 5979 (2023)
23.
Journal Article
Rengachari, S.; Schilbach, S.; Kaliyappan, T.; Gouge, J.; Zumer, K.; Schwarz, J.; Urlaub, H.; Dienemann, C.; Vannini, A.; Cramer, P.: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II. Nature Structural and Molecular Biology 29, pp. 1159 - 1169 (2022)
24.
Journal Article
Frieg, B.; Antonschmidt, L.; Dienemann, C.; Geraets, J. A.; Najbauer, E. E.; Matthes, D.; de Groot, B. L.; Andreas, L. B.; Becker, S.; Griesinger, C. et al.; Schröder, G. F.: The 3D structure of lipidic fibrils of α-synuclein. Nature Communications 13 (1), 6810 (2022)
25.
Journal Article
Yahya, G.; Menges, P.; Amponsah, P. S.; Ngandiri, D. A.; Schulz, D.; Wallek, A. U.; Kulak, N. A.; Mann, M.; Cramer, P.; Savage, V. et al.; Raeschle, M.; Storchova, Z.: Sublinear scaling of the cellular proteome with ploidy. Nature Communications 13 (1), 6182 (2022)
26.
Journal Article
Xue, L.; Lenz, S.; Zimmermann-Kogadeeva, M.; Tegunov, D.; Cramer, P.; Bork, P.; Rappsilber, J.; Mahamid, J.: Visualizing translation dynamics at atomic detail inside a bacterial cell. Nature 610 (7930), pp. 205 - 211 (2022)
27.
Journal Article
Obeng, E. M.; Fianu, I.; Danquah, M. K.: Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development. Nano Today 46, 101580 (2022)
28.
Journal Article
Frieg, B.; Geraets, J. A.; Strohaeker, T.; Dienemann, C.; Mavroeidi, P.; Jung, B. C.; Kim, W. S.; Lee, S.-J.; Xilouri, M.; Zweckstetter, M. et al.; Schroeder, G. F.: Quaternary structure of patient-homogenate amplified α-synuclein fibrils modulates seeding of endogenous α-synuclein. Communications Biology 5 (1), 1040 (2022)
29.
Journal Article
de Opakua, A. I.; Geraets, J. A.; Frieg, B.; Dienemann, C.; Savastano, A.; Rankovic, M.; Cima-Omori, M.-S.; Schröder, G. F.; Zweckstetter, M.: Molecular interactions of FG nucleoporin repeats at high resolution. Nature Chemistry 14, pp. 1278 - 1285 (2022)
30.
Journal Article
Antonschmidt, L.; Matthes, D.; Dervişoğlu, R.; Frieg, B.; Dienemann, C.; Leonov, A.; Nimerovsky, E.; Sant, V.; Ryazanov, S.; Giese, A. et al.; Schröder, G.; Becker, S.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature Communications 13, pp. 5385 - 5394 (2022)
31.
Journal Article
Farnung, L.; Ochmann, M.; Garg, G.; Vos, S.; Cramer, P.: Structure of a backtracked hexasomal intermediate of nucleosome transcription. Molecular Cell 82 (17), pp. 3126 - 3134.e7 (2022)
32.
Journal Article
Fietze, T.; Wilk, P.; Kabinger, F.; Anoosheh, S.; Hofer, A.; Lundin, D.; Feiler, C. G.; Weiss, M. S.; Loderer, C.: HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase. Biochemistry 61 (15), pp. 1633 - 1641 (2022)
33.
Journal Article
Xiong, L.; Tolen, E. A.; Choi, J.; Velychko, S.; Caizzi, L.; Velychko, T.; Adachi, K.; MacCarthy, C. M.; Lidschreiber, M.; Cramer, P. et al.; Schöler, H. R.: Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells. eLife 11, e71533 (2022)
34.
Journal Article
Dombrowski, M.; Engeholm, M.; Dienemann, C.; Dodonova, S. O.; Cramer, P.: Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Nature Structural and Molecular Biology 29 (5), pp. 493 - 501 (2022)
35.
Journal Article
Sahu, B.; Hartonen, T.; Pihlajamaa, P.; Wei, B.; Dave, K.; Zhu, F.; Kaasinen, E.; Lidschreiber, K.; Lidschreiber, M.; Daub, C. O. et al.; Cramer, P.; Kivioja, T.; Taipale, J.: Sequence determinants of human gene regulatory elements. Nature Genetics 54 (3), pp. 283 - 294 (2022)
36.
Journal Article
Downes, D. J.; Smith, A. L.; Karpinska, M. A.; Velychko, T.; Rue-Albrecht, K.; Sims, D.; Milne, T. A.; Davies, J. O. J.; Oudelaar, A. M.; Hughes, J. R.: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature Protocols 17 (2), pp. 445 - 475 (2022)
37.
Journal Article
Baar, T.; Dümcke, S.; Gressel, S.; Schwalb, B.; Dilthey, A.; Cramer, P.; Tresch, A.: RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. G3: Genes, Genomes, Genetics 12 (5), jkac054 (2022)
38.
Journal Article
Shao, R.; Kumar, B.; Lidschreiber, K.; Lidschreiber, M.; Cramer, P.; Elsässer, S. J.: Distinct transcription kinetics of pluripotent cell states. Molecular Systems Biology 18 (1), e10407 (2022)
39.
Journal Article
Fianu, I.; Chen, Y.; Dienemann, C.; Dybkov, O.; Linden, A.; Urlaub, H.; Cramer, P.: Structural basis of Integrator-mediated transcription regulation. Science 374 (6569), pp. 883 - 887 (2021)
40.
Journal Article
Kokic, G.; Wagner, F. R.; Chernev, A.; Urlaub, H.; Cramer, P.: Structural basis of human transcription–DNA repair coupling. Nature 598 (7880), pp. 368 - 372 (2021)
41.
Journal Article
Aibara, S.; Dienemann, C.; Cramer, P.: Structure of an inactive RNA polymerase II dimer. Nucleic Acids Research 49 (18), pp. 10747 - 10755 (2021)
42.
Journal Article
García-Martínez, J.; Medina, D. A.; Bellvís, P.; Sun, M.; Cramer, P.; Chávez, S.; Pérez-Ortín, J. E.: The total mRNA concentration buffering system in yeast is global rather than gene-specific. RNA 27 (10), pp. 1281 - 1290 (2021)
43.
Journal Article
Güttler, T.; Aksu, M.; Dickmanns, A.; Stegmann, K. M.; Gregor, K.; Rees, R.; Taxer, W.; Rymarenko, O.; Schünemann, J.; Dienemann, C. et al.; Gunkel, P.; Mussil, B.; Krull, J.; Teichmann, U.; Groß, U.; Cordes, V.; Dobbelstein, M.; Görlich, D.: Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies. EMBO Journal 40 (19), e107985 (2021)
44.
Journal Article
Bhatta, A.; Dienemann, C.; Cramer, P.; Hillen, H.: Structural basis of RNA processing by human mitochondrial RNase P. Nature Structural and Molecular Biology 28 (9), pp. 713 - 723 (2021)
45.
Journal Article
Cramer, P.: AlphaFold2 and the future of structural biology. Nature Structural and Molecular Biology 28 (9), pp. 704 - 705 (2021)
46.
Journal Article
Kabinger, F.; Stiller, C.; Schmitzova, J.; Dienemann, C.; Kokic, G.; Hillen, H. S.; Höbartner, C.; Cramer, P.: Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nature Structural and Molecular Biology 28 (9), pp. 740 - 746 (2021)
47.
Journal Article
Jochheim, F. A.; Tegunov, D.; Hillen, H. S.; Schmitzova, J.; Kokic, G.; Dienemann, C.; Cramer, P.: The structure of a dimeric form of SARS-CoV-2 polymerase. Communications Biology 4, 999 (2021)
48.
Journal Article
Zumer, K.; Maier, K. C.; Farnung, L.; Jaeger, M. G.; Rus, P.; Winter, G.; Cramer, P.: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Molecular Cell 81 (15), pp. 3096 - 3109.e8 (2021)
49.
Journal Article
Wang, H.; Xiong, L.; Cramer, P.: Structures and implications of TBP–nucleosome complexes. Proceedings of the National Academy of Sciences of the USA 118 (30), e2108859118 (2021)
50.
Journal Article
Schilbach, S.; Aibara, S.; Dienemann, C.; Grabbe, F.; Cramer, P.: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. Cell 184 (15), pp. 4064 - 4072.e28 (2021)
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