Danev Lab   Advanced Structural Studies
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2024

Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCrJ (2024)

2023

Burger WAC, Pham V, Vuckovic Z, Powers AS, Mobbs JI, Laloudakis Y, Glukhova A, Wootten D, Tobin AB, Sexton PM, Paul SM, Felder CC, Danev R, Dror RO, Christopoulos A, Valant C, Thal DM. Xanomeline displays concomitant orthosteric and allosteric binding modes at the M4 mAChR. Nat Commun (2023)
Cao J, Belousoff MJ, Gerrard E, Danev R, Fletcher MM, Dal Maso E, Schreuder H, Lorenz K, Evers A, Tiwari G, Besenius M, Li Z, Johnson RM, Wootten D, Sexton PM. Structural insight into selectivity of amylin and calcitonin receptor agonists. Nat Chem Biol (2023)
Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife (2023)
Danev R, 吉川 雅英 「電子線トモグラフィー」, In: クライオ電子顕微鏡ハンドブック, 難波 啓一 (著, 監修), 加藤 貴之 (著, 監修), 牧野 文信 (著, 監修), NTS inc. (2023)
Eisenstein F, Yanagisawa H, Kashihara H, Kikkawa M, Tsukita S, Danev R. Parallel cryo electron tomography on in situ lamellae. Nat Methods (2023)

2022

Piper SJ, Deganutti G, Lu J, Zhao P, Liang YL, Lu Y, Fletcher MM, Hossain MA, Christopoulos A, Reynolds CA, Danev R, Sexton PM, Wootten D. Understanding VPAC receptor family peptide binding and selectivity. Nat Commun (2022)
Cao J, Belousoff MJ, Liang YL, Johnson RM, Josephs TM, Fletcher MM, Christopoulos A, Hay DL, Danev R, Wootten D, Sexton PM. A structural basis for amylin receptor phenotype. Science (2022)
Deganutti G, Liang Y-L, Zhang X, Khoshouei M, Clydesdale L, Belousoff MJ, Venugopal H, Truong TT, Glukhova A, Keller AN, Gregory KJ, Leach K, Christopoulos A, Danev R, Reynolds CA, Zhao P, Sexton PM, Wootten D. Dynamics of GLP-1R peptide agonist engagement are correlated with kinetics of G protein activation. Nat Commun (2022)
Cary BP, Deganutti G, Zhao P, Truong TT, Piper SJ, Liu X, Belousoff MJ, Danev R, Sexton PM, Wootten D, Gellman SH. Structural and Functional Diversity among Agonist-Bound States of the GLP-1 Receptor. Nat Chem Biol (2022)

2021

Johnson RM, Zhang X, Piper SJ, Nettleton TJ, Vandekolk TH, Langmead CJ, Danev R, Sexton PM, Wootten D. Cryo-EM structure of the dual incretin receptor agonist, peptide-19, in complex with the glucagon-like peptide-1 receptor. Biochem Biophys Res Commun (2021)
Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O'Sullivan K, Chia LY, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, White PJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Imlach WL, Christopoulos A. Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia. Nature (2021)
Danev R, Belousoff M, Liang Y-L, Zhang X, Eisenstein F, Wootten D, Sexton PM. Routine sub-2.5 Å cryo-EM structure determination of GPCRs. Nat Commun (2021)
Mobbs JI, Belousoff MJ, Harikumar KG, Piper SJ, Xu X, Furness SGB, Venugopal H, Christopoulos A, Danev R, Wootten D, Thal DM, Miller LJ, Sexton PM. Structures of the human cholecystokinin 1 (CCK1) receptor bound to Gs and Gq mimetic proteins provide insight into mechanisms of G protein selectivity. PLoS Biol (2021)
Zhang X, Belousoff MJ, Liang YL, Danev R, Sexton PM, Wootten D. Structure and dynamics of semaglutide- and taspoglutide-bound GLP-1R-Gs complexes. Cell Rep (2021)
Danev R, Yanagisawa H, Kikkawa M. Cryo-EM Performance Testing of Hardware and Data Acquisition Strategies. Microscopy (2021)
Danev R. Practical considerations: defocus, stigmation, coma-free illumination, and phase plates. In: Glaeser RM, Nogales E, Chiu W, editors. Single-particle Cryo-EM of Biological Macromolecules. IOP Publishing (2021)
Zhang X, Johnson RM, Drulyte I, Yu L, Kotecha A, Danev R, Wootten D, Sexton PM, Belousoff MJ. Evolving cryo-EM structural approaches for GPCR drug discovery. Structure (2021)
Josephs TM, Belousoff MJ, Liang YL, Piper SJ, Cao J, Garama DJ, Leach K, Gregory KJ, Christopoulos A, Hay DL, Danev R, Wootten D, Sexton PM. Structure and dynamics of the CGRP receptor in apo and peptide-bound forms. Science (2021)

2020

Zhang X, Belousoff MJ, Zhao P, Kooistra AJ, Truong TT, Ang SY, Underwood CR, Egebjerg T, Šenel P, Stewart GD, Liang YL, Glukhova A, Venugopal H, Christopoulos A, Furness SGB, Miller LJ, Reedtz-Runge S, Langmead CJ, Gloriam DE, Danev R, Sexton PM, Wootten D. Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists. Mol Cell (2020)
Danev R. Electrons receive individual treatment with electron-event representation. IUCrJ (2020)
Dong M, Deganutti G, Piper SJ, Liang Y-L, Khoshouei M, Belousoff MJ, Harikumar KG, Reynolds CA, Glukhova A, Furness SGB, Christopoulos A, Danev R, Wootten D, Sexton PM, Miller LJ. Structure and dynamics of the active Gs-coupled human secretin receptor. Nat. Commun. (2020)
Buijsse B, Trompenaars P, Altin V, Danev R, Glaeser RM. Spectral DQE of the Volta phase plate. Ultramicroscopy (2020)
Danev R, Iijima H, Matsuzaki M, Motoki S. Fast and accurate defocus modulation for improved tunability of cryo-EM experiments. IUCrJ (2020)
Chang R, Zhang X, Qiao A, Dai A, Belousoff MJ, Tan Q, Shao L, Zhong L, Lin G, Liang YL, Ma L, Han S, Yang D, Danev R, Wang MW, Wootten D, Wu B, Sexton PM. Cryo-electron microscopy structure of the glucagon receptor with a dual-agonist peptide. J Biol Chem. (2020)
Boopathi R, Danev R, Khoshouei M, Kale S, Nahata S, Ramos L, Angelov D, Dimitrov S, Hamiche A, Petosa C, Bednar J. Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends. Nucleic Acids Res. (2020)
Liang YL, Belousoff MJ, Fletcher MM, Zhang X, Khoshouei M, Deganutti G, Koole C, Furness SGB, Miller LJ, Hay DL, Christopoulos A, Reynolds CA, Danev R, Wootten D, Sexton PM. Structure and Dynamics of Adrenomedullin Receptors AM1 and AM2 Reveal Key Mechanisms in the Control of Receptor Phenotype by Receptor Activity-Modifying Proteins. ACS Pharmacol. Transl. Sci. (2020)
Liang Y-L, Belousoff MJ, Zhao P, Koole C, Fletcher MM, Truong TT, Julita V, Christopoulos G, Xu HE, Zhang Y, Khoshouei M, Christopoulos A, Danev R, Sexton PM, Wootten D. Toward a Structural Understanding of Class B GPCR Peptide Binding and Activation. Mol. Cell (2020)
Zhao P, Liang Y-L, Belousoff MJ, Deganutti G, Fletcher MM, Willard FS, Bell MG, Christe ME, Sloop KW, Inoue A, Truong TT, Clydesdale L, Furness SGB, Christopoulos A, Wang M-W, Miller LJ, Reynolds CA, Danev R, Sexton PM, Wootten D. Activation of the GLP-1 receptor by a non-peptidic agonist. Nature (2020)

2019

Danev R. Electrons see the light. Nat. Methods (2019)
Eisenstein F, Danev R, Pilhofer M. Improved applicability and robustness of fast cryo-electron tomography data acquisition. J. Struct. Biol. (2019)
Danev R, Yanagisawa H, Kikkawa M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions. Trends Biochem. Sci. (2019)
Majumder P, Rudack T, Beck F, Danev R, Pfeifer G, Nagy I, Baumeister W. Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Proc. Natl. Acad. Sci. (2019)

2018

Draper-Joyce CJ, Khoshouei M, Thal DM, Liang YL, Nguyen ATN, Furness SGB, Venugopal H, Baltos J, Plitzko JM, Danev R, Baumeister W, May LT, Wootten D, Sexton P, Glukhova A, Christopoulos A. Structure of the adenosine-bound human adenosine A1 receptor–Gi complex. Nature (2018)
Liang, YL, Khoshouei M, Glukhova A, Furness SGB, Zhao P, Clydesdale L, Koole C, Truong TT, Thal DM, Lei S, Radjainia M, Danev R, Baumeister W, Wang MW, Miller LJ, Christopoulos A, Sexton PM, Wootten D. Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor–Gs complex. Nature (2018)
Von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Ménétret JF, Klaholz BP. Volta phase plate data collection facilitates image processing and cryo-EM structure determination. J. Struct. Biol. (2018)

2017

Gipson P, Fukuda Y, Danev R, Lai Y, Chen DH, Baumeister W, Brunger AT. Morphologies of synaptic protein membrane fusion interfaces. Proc. Natl. Acad. Sci. (2017)
Khoshouei M, Danev R, Plitzko JM, Baumeister W. Revisiting the Structure of Hemoglobin and Myoglobin with Cryo-Electron Microscopy. J. Mol. Biol. (2017)
Danev R, Baumeister W. Expanding the boundaries of cryo-EM with phase plates. Curr. Opin. Struct. Biol. (2017)
Khoshouei M, Radjainia M, Baumeister W, Danev R. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate. Nat. Commun. (2017)
Liang YL, Khoshouei M, Radjainia M, Zhang Y, Glukhova A, Tarrasch J, Thal DM, Furness SGB, Christopoulos G, Coudrat T, Danev R, Baumeister W, Miller LJ, Christopoulos A, Kobilka BK, Wootten D, Skiniotis G, Sexton PM. Phase-plate cryo-EM structure of a class B GPCR-G-protein complex. Nature (2017)
Danev R, Tegunov D, Baumeister W. Using the Volta phase plate with defocus for cryo-EM single particle analysis. eLife (2017)
Khoshouei M, Pfeffer S, Baumeister W, Förster F, Danev R. Subtomogram analysis using the Volta phase plate. J. Struct. Biol. 197, 94-101 (2017)

2016

Chua EYD, Vogirala VK, Inian O, Wong ASW, Nordenskiöld L, Plitzko JM, Danev R, Sandin S. 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM. Nucl. Acids Res. (2016)
Danev R, Baumeister W. Cryo-EM single particle analysis with the Volta phase plate. eLife (2016)
Mahamid J, Pfeffer S, Schaffer M, Villa E, Danev R, Cuellar LK, Förster F, Hyman AA, Plitzko JM, Baumeister W. Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science (2016)
Khoshouei M, Radjainia M, Phillips AJ, Gerrard JA, Mitra AK, Plitzko JM, Baumeister W, Danev R. Volta phase plate cryo-EM of the small protein complex Prx3. Nat. Commun. (2016)

2015

Kishchenko G, Danev R, Fisher R, He J, Hsieh C, Marko M, Sui H. Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM. J. Struct. Biol. (2015)
Fukuda Y, Laugks U, Lučić V, Baumeister W, Danev R. Electron cryotomography of vitrified cells with a Volta phase plate. J. Struct. Biol. (2015)
Asano S, Fukuda Y, Beck F, Aufderheide A, Förster F, Danev R, Baumeister W. A molecular census of 26S proteasomes in intact neurons. Science (2015)

2014

Danev R, Buijsse B, Khoshouei M, Plitzko J, Baumeister W. Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci. (2014)











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