Our publications

    2018

  • J. Zivanov, T. Nakane, B. Forsberg, D. Kimanius, W.J.H. Hagen, E. Lindahl & S.H.W. Scheres (2018)
    "RELION-3: new tools for automated high-resolution cryo-EM structure determination"
    bioRxiv 421123
  • B. Falcon, W. Zhang, M. Schweighauser, A.G. Murzin, R. Vidal, H.J. Garringer, B. Ghetti, S.H.W. Scheres & M. Goedert (2018)
    "Tau filaments from multiple cases of sporadic and inherited Alzheimer's disease adopt a common fold"
    bioRxiv 411215
  • J. Zivanov, T. Nakane & S.H.W. Scheres (2018)
    "A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis"
    bioRxiv 384537
  • B. Falcon, W. Zhang, A.G. Murzin, G. Murshudov, H.J. Garringer, R. Vidal, R.A. Crowther, B. Ghetti, S.H.W. Scheres & M. Goedert (2018)
    "Structures of filaments from Pick's disease reveal a novel tau protein fold"
    Nature 561, 127-140, bioRxiv 302216
  • T. Nakane, D. Kimanius, E. Lindahl & S.H.W. Scheres (2018)
    "Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION"
    eLife 7:e36861, bioRxiv 286856
  • O. Salih, S. He, S. Planamente, L. Stach, J.T. MacDonald, E. Manoli, S.H.W. Scheres, A. Filloux & P.S. Freemont (2018)
    "Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa"
    Structure 26:329-336
  • 2017

  • C. Gati, A. Stetsenko, D.J. Slotboom, S.H.W. Scheres & A. Guskov (2017)
    "The structural basis of proton driven zinc transport by ZntB"
    Nat. Commun. 8:1313
  • F.J.D. Alvarez, S. He, J.R. Perilla, S. Jang, K. Schulten, A.N. Engelman, S.H.W. Scheres & P. Zhang (2017)
    "CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction"
    Science Adv. 3:e1701264
  • S.H.W. Scheres & K. Nagai (2017)
    "CryoEM structures of spliceosomal complexes reveal the molecular mechanism of pre-mRNA splicing"
    Curr. Opin. Struc. Biol. 46, 130-139
  • A.W.P. Fitzpatrick, B. Falcon, S. He, A.G. Murzin, G. Murshudov, H.J. Garringer, R.A. Crowther, B. Ghetti, M. Goedert & S.H.W. Scheres (2017)
    "Cryo-EM structures of tau filaments from Alzheimer's disease"
    Nature 547, 185-190
  • A.W.P. Fitzpatrick, S. Llabres, A. Neuberger, J.N. Blaza, X.-C. Bai, U. Okada, S. Murakami, H.W. van Veen, U. Zachariae, S.H.W. Scheres, B.F. Luisi & D. Du (2017)
    "Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump"
    Nat. Microbiol. 2:17070
  • W. Wong, X.-C. Bai, B.E. Sleebs, T. Triglia, A. Brown, J.K. Thompson, K.E. Jackson, E. Hanssen, D.S. Marapana, I.S. Fernandez, S.A. Ralph, A.F. Cowman, S.H. W. Scheres & J. Baum (2017)
    "Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis"
    Nat. Microbiol. 2:17031
  • A. Boland, T.G. Martin, Z. Zhang, J. Yang, L. Chang, S.H. W. Scheres & D. Barford (2017)
    "Cryo-EM structure of a metazoan separase-securin complex at near-atomic resolution"
    Nat. Struct. Mol. Biol. 24, 414-418
  • S. He & S.H.W. Scheres (2017)
    "Helical reconstruction in RELION"
    J. Struct. Biol. 198, 163-176, bioRxiv 095034
  • Y. Li, M. Zhou,Q Hu,X.-C. Bai, W. Huang, S.H.W. Scheres & Y. Shi (2017)
    "Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme"
    Proc. Natl. Acad. Sci. U S A 114(7), 1542-1547
  • R. Fernandez-Leiro, J. Conrad, J.-C. Yang, S.M.V. Freund, S.H.W. Scheres & M.H. Lamers (2017)
    "Self-correcting mismatches during high-fidelity DNA replication"
    Nat. Struct. Mol. Biol. 24, 140-143
  • R. Fernandez-Leiro & S.H.W. Scheres (2017)
    "A pipeline approach to single-particle processing in RELION"
    Acta Cryst. D73, 496-502, bioRxiv 095034
  • 2016

  • D. Kimanius, B.O. Forsberg, S.H.W. Scheres & E. Lindahl (2016)
    "Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2"
    eLife 5:e18722, bioRxiv 059717
  • T.G. Martin, T.A. Bharat, A.C. Joerger, X.-C. Bai, F. Praetorius, A.R. Fersht, H. Dietz & S.H.W. Scheres (2016)
    "Design of a molecular support for cryo-EM structure determination"
    Proc. Natl. Acad. Sci. U S A 113(47), E7456-E7463
  • J. Lowe, S. He, S.H.W. Scheres & C.G. Savva (2016)
    "X-ray and cryo-EM structures of monomeric and filamentous actin-like protein MamK reveal changes associated with polymerization"
    Proc. Natl. Acad. Sci. U S A 113(47), 13396-13401
  • T.A. Bharat & S.H.W. Scheres (2016)
    "Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION."
    Nat. Protoc. 11, 2054-65, bioRxiv 030544
  • R. Fernandez-Leiro & S.H.W. Scheres (2016)
    "Unravelling biological macromolecules with cryo-electron microscopy"
    Nature 537, 339-346.
  • S.H.W. Scheres (2016)
    "Processing of Structurally Heterogeneous Cryo-EM Data in RELION"
    Meth. Enzym. 579, 125-157
  • T.H. Nguyen, W.P. Galej, X.-C. Bai, C. Oubridge, A.J. Newman, S.H.W. Scheres & K. Nagai (2016)
    "Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution"
    Nature 530, 298-302.
  • 2015

  • X.-C. Bai, E. Rajendra, G. Yang, Y. Shi & S.H.W. Scheres (2015)
    "Sampling the conformational space of the catalytic subunit of human gamma-secretase"
    eLife 3:e11182, bioRxiv 025890
  • R. Fernandez-Leiro, J. Conrad, S.H.W. Scheres & M.H. Lamers (2015)
    "cryo-EM structures of the E. coli replicative DNA polymerase reveal dynamic interactions with clamp, exonuclease and tau"
    eLife 4:e11134.
  • M. Zhou, Y. Li, Q. Hu, X.-C. Bai, W. Huang, C. Yan, S.H.W. Scheres & Y Shi (2015)
    "Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1"
    Genes Dev. 29, 2349-61.
  • X.-C. Bai, C. Yan, G. Yang, P. Lu, D. Ma, L. Sun, R. Zhou, S.H.W. Scheres & Y Shi (2015)
    "An atomic structure of human gamma-secretase"
    Nature 525, 212-217.
  • T.A. Bharat, C.J. Russo, J. Loewe, L.A. Passmore & S.H.W. Scheres (2015)
    "Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging."
    Structure 23, 1743-1753
  • T.H. Nguyen, W.P. Galey, X.-C. Bai, C.G. Savva, A.J. Newman, S.H.W. Scheres & K. Nagai (2015)
    "The architecture of the spliceosomal U4/U6.U5 tri-snRNP"
    Nature 253, 47-52.
  • E. Nogales & S.H.W. Scheres (2015)
    "Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity"
    Mol. Cell 58, 677-689.
  • Y. Pang, X.-C. Bai, C. Yan, Q. Hao, Z. Chen, J.-W. Wang, S.H.W. Scheres & Y Shi (2015)
    "Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila"
    Genes Dev. 29, 277-287.
  • A. Amunts, A. Brown, J. Toots, S.H.W. Scheres & V. Ramakrishnan (2015)
    "The structure of the human mitochondrial ribosome"
    Science 348, 95-98.
  • S.H.W. Scheres (2015)
    "Semi-automated selection of cryo-EM particles in RELION-1.3"
    J. Struc. Biol. 189, 114-122.
  • Z. Yan, X.-C. Bai, C. Yan, J. Wu, Z. Li, T. Xie, W. Peng, C. Yin, X. Li, S.H.W. Scheres, Y. Shi & N. Yan (2015)
    "Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution"
    Nature 517, 50-55.
  • X.-C. Bai, G. McMullan & S.H.W. Scheres (2015)
    "How cryo-EM is revolutionizing structural biology"
    Trends in Biochemical Sciences 40, 49-57.
  • C. Wood, T. Burnley, A. Patwardhan, S.H.W. Scheres, M. Topf, A. Roseman & M. Winn (2015)
    "Collaborative computational project for electron cryo-microscopy"
    Acta Cryst. D 71, 123-126.
  • 2014

  • A. Brown, A. Amunts, X.-C. Bai, Y. Sugimoto, P.C. Edwards, G. Murshudov, S.H.W. Scheres & V. Ramakrishnan (2014)
    "Structure of the large ribosomal subunit from human mitochondria"
    Science 346, 718-722.
  • S.H.W. Scheres (2014)
    "Beam-induced motion correction for sub-megadalton cryo-EM particles"
    eLife 3:e03665. Comments on this paper: eLife insight.
  • P. Lu, X.-C. Bai, D. Ma, T. Xie, C. Yan, L. Sun, G. Yang, Y. Zhao, R. Zhou, S.H.W. Scheres & Y. Shi (2014)
    "Three-dimensional structure of human gamma-secretase"
    Nature 512, 166-170. Comments on this paper: Preview in Cell , Faculty of 1000.
  • R.M. Voorhees, I.S. Fernandez, S.H.W. Scheres & R.S. Hegde (2014)
    "Structure of the mammalian ribosome-Sec61 complex to 3.4 Angstrom resolution"
    Cell 157, 1632-1643. Comments on this paper: Faculty of 1000.
  • W. Wong, X.-C. Bai, A. Brown, I.S. Fernandez, E. Hanssen, M. Condron, Y. Hong Tan, J. Baum & S.H.W. Scheres (2014)
    "Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine"
    eLife 3:e03080.
  • I.S. Fernandez, X.-C. Bai, G. Murshudov, S.H.W. Scheres & V. Ramakrishnan (2014)
    "Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome"
    Cell 157, 823-831.
  • A. Amunts, A. Brown, X.-C. Bai, J.L. Llacer, T. Hussain, P. Emsley, F. Long, G. Murshudov, S.H.W. Scheres & V. Ramakrishnan (2014)
    "Structure of the Yeast Mitochondrial Large Ribosomal Subunit"
    Science 343, 1485-1489. Comments on this paper: Science perspective, Faculty of 1000.
  • 2013

  • I.S. Fernandez, X.-C. Bai, T. Hussain, A.C. Kelley, J.R. Lorsch, V. Ramakrishnan & S.H.W. Scheres (2013)
    "Molecular architecture of a eukaryotic translational initiation complex"
    Science 342, 6160.
  • S.P. Muench, S.H.W. Scheres, M. Huss, C. Phillips, O. Vitavska, H. Wieczorek, J. Trinick & M.A. Harrison (2013)
    "Subunit Positioning and Stator Filament Stiffness in Regulation and Power Transmission in the V1 Motor of the Manduca sexta V-ATPase"
    J. Mol. Biol. 426, 286-300.
  • S. Chen, G. McMullan, A.R. Faruqi, G.N. Murshudov, J.M. Short, S.H.W. Scheres & R. Henderson (2013)
    "High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy"
    Ultramicroscopy 135, 24-35. Comments on this paper: Faculty of 1000.
  • A. Sauerwald, S. Sandin, G. Cristofari, S.H.W. Scheres, J. Lingner & D. Rhodes (2013)
    "Structure of active dimeric human telomerase"
    Nat. Struct. Mol. Biol. 20, 454-460. Comments on this paper: Faculty of 1000.
  • X.-C. Bai, I.S. Fernandez, G. McMullan & S.H.W. Scheres (2013)
    "Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles"
    eLife 2:e00461. Comments on this paper: eLife Insight, Nature Methods News & Views, Faculty of 1000.
  • 2012

  • A. Patwardhan, J.M. Carazo, B. Carragher, R. Henderson, J.B. Heymann, E. Hill, G.J. Jensen, I. Lagerstedt, C.L. Lawson, S.J. Ludtke, D. Mastronarde, W.J. Moore, A. Roseman, P. Rosenthal, C.O.S. Sorzano, E. Sanz-Garcia, S.H.W. Scheres, S. Subramaniam, J. Westbrook, M. Winn, J.R. Swedlow & G.J. Kleywegt (2012)
    "Data management challenges in three-dimensional EM"
    Nat. Struct. Mol. Biol. 19, 1203-1207.
  • X.-C. Bai, T.G. Martin, S.H.W. Scheres & H. Dietz (2012)
    "Cryo-EM structure of a 3D DNA-origami object"
    Proc. Natl. Acad. Sci. U S A 109, 20012-20017. Comments on this paper: Faculty of 1000.
  • S.H.W. Scheres (2012)
    "RELION: Implementation of a Bayesian approach to cryo-EM structure determination"
    J. Struc. Biol. 180, 519-530.
  • S.H.W. Scheres & S. Chen (2012)
    "Prevention of overfitting in cryo-EM structure determination"
    Nat. Methods 9, 853-854.
  • S.H.W. Scheres (2012)
    "A Bayesian view on cryo-EM structure determination"
    J. Mol. Biol. 415, 406-418.
  • 2010

  • S.H.W. Scheres (2010)
    "Visualizing molecular machines in action: single-particle analysis with structural variability"
    Advances in Protein Chemistry and Structural Biology 81, 89-119
  • S.H.W. Scheres (2010)
    "Classification of structural heterogeneity by maximum-likelihood methods"
    Meth. Enzym. 482, 295-320.
  • F.J. Sigworth, P. Doerschuk, J.M. Carazo & S.H.W. Scheres (2010)
    "An introduction to maximum-likelihood methods in cryo-EM"
    Meth. Enzym. 482, 263-294.
  • pre-LMB

  • R. Melero, S. Rajagopalan, M. Lazaro, A.C. Joerger, T. Brandt, D.B. Veprintsev, G. Lasso, D. Gil, S.H.W. Scheres, J.M. Carazo, A.R. Fersht & M. Valle (2011)
    "Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA"
    Proc. Natl. Acad. Sci. U S A 108, 557-562
  • M. Stolken, F. Beck, T. Haller, R. Hegerl, I. Gutsche, J.M. Carazo, W. Baumeister, S.H.W. Scheres & S. Nickell (2011)
    "Maximum Likelihood based Classification of Electron Tomographic Data"
    J. Struc. Biol. 173, 77-85.
  • J.O. Ortiz, F. Brandt, V.R.F. Matias, L. Sennels, J. Rappsilber, S.H.W. Scheres, M. Eibauer, F.U. Hartl & W. Baumeister (2010)
    "Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ"
    J. Cell. Biol. 190, 613-621. Comments on this paper: Faculty of 1000
  • I. Cuesta, R. Nunez-Ramirez, S.H.W. Scheres, D. Gai, X. Chen, E. Fanning. & J.M. Carazo (2010)
    "Conformational rearrangements of SV40 large-T antigen during early replication events"
    J. Mol. Biol. 397, 1276-1286
  • K. Cheng, N. Ivanova, S.H.W. Scheres, M.Y. Pavlov, J.M. Carazo, H. Hebert, M. Ehrenberg & Martin Lindahl (2010)
    "tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes"
    J. Struc. Biol. 169, 342-348
  • S.H.W. Scheres, R.M. Melero, M. Valle & J.M. Carazo (2009)
    "Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization"
    Structure 17, 1563-1572
  • M.A. Recuero-Checa, A.S. Dore, E. Arias-Palomo, A. Rivera-Calzada, S.H.W. Scheres, J.D. Maman, L.H. Pearl & O. Llorca (2009)
    "Electron Microscopy of Xrcc4 and the DNA ligase IV-Xrcc4 DNA repair complex"
    DNA Repair 8, 1380-1389
  • A.J. Perez-Berna, R. Marabini, S.H.W. Scheres, R. Menendez-Conejero, I.P. Dmitriev, D.T. Curiel, W.F. Mangel, S.J. Flint & C. San Martin (2009)
    "Structure and uncoating of immature adenovirus"
    J. Mol. Biol. 292, 547-557
  • S. Nickell, F. Beck, S.H.W. Scheres, A. Korinek, F. Foerster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, A. Sali, J.M. Plitzko, J.M. Carazo, M. Mann & W. Baumeister (2009)
    "New insights into the molecular architecture of the 26S proteasome"
    Proc. Natl. Acad. Sci. U S A 106, 11943-11947
  • S.H.W. Scheres, & J.M. Carazo (2009)
    "Introducing robustness to maximum likelihood refinement of electron microscopy data"
    Acta Cryst. D65, 672-678
  • S.H.W. Scheres, M. Valle, P. Grob, E. Nogales & J.M. Carazo (2009)
    "Maximum likelihood refinement of electron microscopy data with normalization errors"
    J. Struc. Biol. 166, 234-240
  • P. Julian, A.L. Konevega, S.H.W. Scheres, M. Lazaro, D. Gil, W. Wintermeyer, M.V. Rodnina & M. Valle (2008)
    "Structure of Ratcheted Ribosomes with tRNAs in Hybrid States"
    Proc. Natl. Acad. Sci. U S A 105, 16924-16927
  • J. Cuellar, J. Martin-Benito, S.H.W. Scheres, R. Sousa, F. Moro, E. Lopez-Viñas, P. Gomez-Puertas, A. Muga, J.L. Carrascosa & J.M. Valpuesta (2008)
    "The structure of a CCT:Hsc70NBD complex suggests a mechanism for Hsp70 delivery of substrates to the chaperonin"
    Nat. Struct. Mol. Biol. 15, 858-864. Comments on this paper: Faculty of 1000
  • S.H.W. Scheres, G.T. Herman & J.M. Carazo (2008) PDF
    "Exploring the conformational flexibility of macromolecular machines"
    Mathematical Methods in Biomedical Imaging and Intensity-Modulated Radiation Therapy (IMRT)
    Y. Censor, M. Jiang and A.K. Louis (Editors), Edizioni della Normale, Pisa, Italy, 349-365
  • S.H.W. Scheres, R. Nuñez-Ramirez, C.O.S. Sorzano, J.M. Carazo & R. Marabini (2008)
    "Image processing for electron microscopy single-particle analysis using Xmipp"
    Nat. Protoc. 3, 977-990
  • S.H.W. Scheres, R. Nuñez-Ramirez, Y. Gomez-Llorente, C. San Martin, P.P.B. Eggermont & J.M. Carazo (2007)
    "Modelling experimental image formation for likelihood-based classification of electron microscopy data"
    Structure 15, 1167-1177
  • X. Agirrezabala, J.A. Velazquez-Muriel, P. Gomez-Puertas, S.H.W. Scheres, J.M. Carazo & J.L. Carrascosa (2007)
    "Quasi-atomic model of bacteriophage T7 procapsid shell: insights into the structure and evolution of a basic fold"
    Structure 15, 461-472
  • S.H.W. Scheres, H. Gao, M. Valle, G.T. Herman, P.P.B. Eggermont, J. Frank & J.M. Carazo (2007)
    "Disentangling Conformational States of Macromolecules in 3D-EM through Likelihood Optimization"
    Nat. Methods 4, 27-29. Comments on this paper: News & Views Nature Methods, Faculty of 1000
  • C.O.S. Sorzano, R. Marabini, A. Pascual-Montano, S.H.W. Scheres & J.M. Carazo (2006)
    "Optimization problems in electron microscopy of single particles"
    Annals of Operations Research 148(1), 133-165
  • S.H.W. Scheres, M. Valle & J.M. Carazo (2005)
    "Fast maximum-likelihood refinement of electron microscopy images"
    Bioinformatics 21 (Suppl. 2), ii243-ii244
  • S.H.W. Scheres, A.J. Merino, C.O.S. Sorzano & J.M. Carazo (2005)
    "Grid Computing in 3D-EM Image Processing Using Xmipp"
    18th IEEE Symposium on Computer-Based Medical Systems pp. 561-563
  • S.H.W. Scheres, R. Marabini, S. Lanzavecchia, F. Cantele, T. Rutten, S.D. Fuller, J.M. Carazo, R.M. Burnett & C. San Martin (2005)
    "Classification of single projection reconstructions for cryo-electron microscopy data of icosahedral viruses"
    J. Struc. Biol. 151(1), 79-91
  • S.H.W. Scheres, M. Valle, R. Nuñez, R. Marabini, C.O.S. Sorzano, G.T. Herman & J.M. Carazo (2005)
    "Maximum-likelihood multi-reference refinement for electron microscopy images"
    J. Mol. Biol. 348(1), 139-149
  • J. Velázquez-Muriel, C.O.S. Sorzano, S.H.W. Scheres & J.M. Carazo (2005)
    "SPI-EM: Towards a tool for predicting CATH superfamilies in 3D-EM maps"
    J. Mol. Biol. 345(4), 759-771
  • S.H.W. Scheres< & P. Gros (2004)
    "The potentials of conditional optimization in phasing and model building of protein-structures"
    Acta Cryst. D60, 2202-2209
  • C.O.S. Sorzano, R. Marabini, J. Velázquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo & A. Pascual-Montano (2004)
    "XMIPP: a new generation of an open-source image processing package for Electron Microscopy"
    J. Struc. Biol. 148(2), 194-204
  • S.H.W. Scheres & P. Gros (2003)
    "Development of a force field for conditional optimization of protein structures"
    Acta Cryst. D59, 483-446
  • S.H.W. Scheres & P. Gros (2001)
    "Conditional optimization: a new formalism for protein structure refinement"
    Acta Cryst. D57, 1820-1828
  • R.B.G. Ravelli, M.L. Raves, S.H.W. Scheres, A. Schouten & J. Kroon (1999)
    "Ab initio structure determination of low-molecular-weight compounds using Laue synchrotron radiation Laue diffraction"
    J. Synchrotron Rad.
    6, 19-28

Featured highlights

Near-atomic ribosome maps

Bai et al. (2013) eLife 2:e00461

A combination of direct-electron detection and statistical movie processing to compensate for beam-induced movement allows ribosome structures to be determined from cryo-EM data to resolutions that were previously only attainable by X-ray crystallography.

Bayesian view on cryo-EM

Scheres (2012) J. Mol. Biol. 415, 406-418 (2012)

The Bayesian framework expresses the entire reconstruction workflow in one optimization target and learns the corresponding parameters from the data. Thereby, the need for user expertise is alleviated and arbitrariness is reduced. Results indicate that the Bayesian approach reduces overfitting, yields objective resolution estimates, and detects smaller classes in structurally heterogeneous data sets.