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A modular platform for engineering function of natural and synthetic biomolecular condensates
K. Lasker*, S. Boeynaems*, V. Lam, E. Stainton, M. Jacquemyn, D. Daelemans, E. Villa, A.S. Holehouse, A. Gitler‡, L. Shapiro‡
bioRxiv, 2021. DOI: 10.1101/2021.02.03.429226



A Cytoskeletal Vortex Drives Phage Nucleus Rotation During Jumbo Phage Replication in E. coli
Erica A. Birkholz, Thomas G. Laughlin, Sergey Suslov, Emily Armbruster, Jina Lee, Johannes Wittmann, Kevin D. Corbett, Elizabeth Villa, Joe Pogliano

Cell Reports, 2022. DOI:10.1016/j.celrep.2022.111179

Architecture and self-assembly of the jumbo bacteriophage nuclear shell.
T. G. Laughlin*, A. Deep*, A. M. Prichard, C. Seitz, Y. Gu, E. Enustun, S. Suslov, K. Khanna, E. A. Birkholz, E. Armbruster, J. A. McCammon, R. E. Amaro, J. Pogliano‡, K. D. Corbett‡, E. Villa‡.
bioRxiv, 2022. DOI:10.1101/2022.02.14.480162
Nature, 2022 DOI:10.1038/s41586-022-05013-4

Revealing bacterial cell biology using cryo-electron tomography
K. Khanna and E. Villa
Curr. Opin. Struct. Biol., 2022. DOI: 10.1016/

Subcellular Organization of Viral Particles During Maturation of Nucleus-Forming Jumbo Phage
V. Chaikeeratisak, K. Khanna, K.T. Nguyen, M.E. Egan, E. Enustun, E. Armbruster, K. Pogliano, E. Villa‡, J. Pogliano‡
bioRxiv, 2021. DOI:10.1101/2021.04.26.441357
Science Advances. 2022. DOI: 10.1126/sciadv.abj9670

Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex
C. W. Akey*‡, D. Singh*, C. Ouch*, I. Echeverria*, I. Nudelman, J. M. Varberg, Z. Yu, F. Fang, Y. Shi, J. Wang, D. Salzberg, K. Song, C. Xu, J. C. Gumbart, S. Suslov, J. Unruh, S.L. Jaspersen, B.T. Chait, A. Sali, J. Fernandez-Martinez‡, S. J. Ludtke‡, E. Villa‡, M. P. Rout‡
bioRxiv, 2021. DOI: 10.1101/2021.10.29.466335
Cell. 2022. DOI: 10.1016/j.cell.2021.12.015
Read a Preview by Megan McCarthy and Patrick Lusk.

Entropy Regularized Deconvolution of Cellular Cryo-Transmission Electron Tomograms
M. Croxford, M. Elbaum, M. Arigovindan, Z. Kam, D. A. Agard, E. Villa‡, J. Sedat‡
bioRxiv, 2020. DOI:10.1101/2021.04.26.441469
PNAS, 2021. DOI: 10.1073/pnas.2108738118

Selective transport of fluorescent proteins into the phage nucleus
K.T. Nguyen, J. Sugie, K. Khanna, E.E. MacKennon, E.A. Birkholz, J. Lee, C. Beierschmitt, E. Villa, J. Pogliano
bioRxiv, 2020. DOI:10.1101/2020.11.25.398438
PLoS ONE, 2021. DOI:10.1371/journal.pone.0251429

Asymmetric localization of the cell division machinery during Bacillus subtilis sporulation
K. Khanna, J. Lopez-Garrido, J. Sugie, K. Pogliano‡, E. Villa‡
bioRxiv, 2020.
eLife, 2021. DOI: 10:e62204 DOI: 10.7554/eLife.62204

Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps
B.R. Gilbert, Z.R. Thornburg, V. Lam, F.M. Rashid, J.I. Glass, E. Villa, R.T. Dame, and Z. Luthey-Schulten1
Front. Mol. Biosci. 2021. DOI:10.3389/fmolb.2021.644133

The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein
S. Lu*,  Q. Ye*, D. Singh, E. Villa, D.W. Cleveland‡, K. D. Corbett‡
bioRxiv, 2020.
Nature Communications, 2021. DOI: 10.1038/s41467-020-20768-y

Practical Approaches for Cryo-FIB Milling and Applications for Cellular Cryo-Electron Tomography.
V. Lam V., E. Villa.
In: Gonen T., Nannenga B.L. (eds) cryoEM. Methods in Molecular Biology, vol 2215, 2021. Humana, New York, NY. DOI:10.1007/978-1-0716-0966-8_3

HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells
H. Yu, S. Lu, K. Gasior, D. Singh, O. Tapia, S. Vazquez-Sanchez, D. Toprani, M. S. Beccari, J. R. Yates III, S. Da Cruz, J. M. Newby, M. Larfaga, A. S. Gladfelter, E. Villa, D. W. Cleveland
bioRxiv, 2020.
Science, 2020. DOI: 10.1126/science.abb4309

The in situ structure of Parkinson’s disease-linked LRRK2
R. Watanabe*,  R. Buschauer*,  J. Böhning*, M. Audagnotto, K. Lasker, T.W. Lu, D. Boassa, S. Taylor, E. Villa.
bioRxiv, 2019. DOI:10.1101/837203
Cell, 2020. DOI: 10.1016/j.cell.2020.08.004

Parkinson’s Disease-linked LRRK2 structure and model for microtubule interaction
C. K. Deniston*, J. Salogiannis*, S. Mathea*, D. M. Snead, I. Lahiri, O. Donosa, R. Watanabe, J. Böhning, A. K Shiau, S. Knapp, E. Villa, S. L. Reck-Peterson‡, A. E. Leschziner‡
bioRxiv, 2020. DOI: 10.1101/2020.01.06.895367
Nature,  2020. DOI: 10.1038/s41586-020-2673-2.

Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography
F. R. Wagner*, R. Watanabe*, R. Schampers, D. Singh, H. Persoon, M. Schaffer,  P. Fruhstorfer, J. Plitzko, E. Villa
Nature Protocols,  2020. DOI:10.1038/s41596-020-0320-x

A novel vibriophage exhibits inhibitory activity against host protein synthesis machinery
K. Thammatinna, M. E. Egan, H. H. Htoo, K. Khanna, J. Sugie, J.F. Nideffer, E. Villa, A. Tassanakajon, J. Pogliano, P. Nonejuie, V. Chaikeeratisak
Sci Rep 10, 2347, 2020. DOI:10.1038/s41598-020-59396-3

Viral Capsid Trafficking along Treadmilling Tubulin Filaments in Bacteria
V. Chaikeeratisak, K. Khanna, K. T. Nguyen, J. Sugie, M. E. Egan, M. L. Erb, A. Vavilina, P. Nonejuie, E. Nieweglowska, K. Pogliano, D. A. Agard, E. Villa‡, J. Pogliano‡.
Cell,  177, 1–10, 2019.

The molecular architecture of engulfment during Bacillus subtilis sporulation
K. Khanna, J. Lopez-Garrido, Z. Zhao, R. Watanabe, Y. Yuan, K. Pogliano‡, E. Villa‡
bioRxiv,  2019. DOI:10.1101/498220
eLife 2019;8:e45257 DOI: 10.7554/eLife.45257.

Chromosome Translocation Inflates Bacillus Forespores and Impacts Cellular Morphology. 
J. Lopez-Garrido, N. Ojkic, K. Khanna, F.R. Wagner, E. Villa, R.G. Endres, K. Pogliano.
Cell 172 (4), 758-770. e14, 2018.

Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cells Simulations.
T.M. Earnest, R. Watanabe, J. E. Stone, J. Mahamid, W. Baumeister, E. Villa, and Z. Luther-Schulten.
Klaus Schulten Memorial Issue, J. Phys. Chem. B. 121:3871–3881, 2017.

Assembly of a nucleus-like structure during viral replication in bacteria.
V. Chaikeeratisak, K. Nguyen, K. Khanna, A.F. Brilot, M.L. Erb, J.K. C. Coker,  A. Vavilina, G.L. Newton, R.Buschauer, K.Pogliano, E.Villa, D.A. Agard,  J. Pogliano.
Science. 355:194-197, 2017.

Visualizing the molecular sociology at the HeLa cell nuclear periphery.
J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev, L. Kuhn-Cuellar, F. Foerster, A. A. Hyman, J. M. Plitzko and W. Baumeister.
Science. 351:969-972, 2016.

A photoactivable multi- inhibitor nanoliposome for tumour control and simultaneous inhibition of treatment escape pathways.
B. Q. Spring, R. B. Sears, L.Z. Zheng, Z. Mai, R. Watanabe, M. E. Sherwood, D. A. Schoenfeld, B. W. Pogue, S. P. Pereira, E. Villa, and T. Hasan.
Nature Nanotechnology11:378, 2016.

Architecture of the RNA polymerase II-Mediator core transcription initiation complex.
C. Plaschka, L. Lariviere, L. Wenzeck, M. Hemann, D. Tegunov, E.V. Petrotchenko, C.H. Borchers, W. Baumeister, F. Herzog, E. Villa, and P. Cramer.
Nature, 518, 2014.

Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography.
B. D. Engel, M. Schaffer, L. K. Cuellar, E. Villa, J.M. Plitzko, W. Baumeister.
eLife, 2014.

Finding the right fit: chiseling structures out of cryo-electron microscopy maps.
E. Villa‡, K. Lasker‡.
Curr. Opin. Struct. Biol., 25:118–25, 2014.

Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography.
E. Villa, M. Schaffer, J.M. Plitzko and W. Baumeister.
Curr. Opin. in Struct. Biol., 23, 771–777, 2013.

Three-dimensional architecture of actin filaments in Listeria monocytogenes comet tails.
M.Jasnin, S. Asano, E. Gouin, R. Hegerl, J.M. Plitzko, E. Villa, et al.
PNAS, 110:20521- 20526, 2013.

Near-atomic resolution structural model of the yeast 26S proteasome.
F. Beck, P. Unverdorben, S. Bohn, A. Schweitzer , G. Pfeifer, E. Sakata, S. Nickell, J.M. Plitzko, E. Villa, W. Baumeister, F. Foerster.
PNAS 109:14870-14875, 2012.

Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution.
J.P. Armache, A.M. Anger, V. Marquez, S. Frackenberg, E. Villa, M. Thomm., R. Beckmann, D.N. Wilson.
NAR 41, 1284–1293, 2013.

Integrative Approaches for Cellular Cryo-electron Tomography: Correlative Imaging and Focused Ion Beam Micromachining.
A. Rigort, E. Villa, F. Baeuerlein, B.D. Engel, and J.M. Plitzko.
Met. Cell. Biology, 111, 259281, 2012.

The structure of human Tripeptidyl peptidase II as determined by a hybrid approach.
A. Schoenegge, E. Villa, F. Foerster, R. Hegerl, J. Peters, W. Baumeister, and B. Rockel.
Structure 20, 593-603, 2012.

Focused ion beam micromachining of eukaryotic cells for cryo-electron tomography.
A. Rigort*, F.J.B. Baeuerlein*, E. Villa, M. Eibauer, T. Laugks, W. Baumeister and J.M. Plitzko.
PNAS 109, 4449-4454, 2012.

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.
K. Lasker, F. Foerster, S. Bohn, T. Walzthoenid, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, and W. Baumeister.
PNAS, 109,1380-1387, 2012.

Dynein achieves processive motion using both stochastic and coordinated stepping.
W. Qiu, N.D. Derr, B.S. Goodman, E. Villa, D. Wu, W. Shih and S.L. Reck-Peterson.
Nat Struct Mol Biol. 19, 193-200, 2012.

Structure determination of macromolecular complexes by cryo-electron microscopy in vitro and in situ.
F. Foerster, E. Villa, D. Thomas, A. Korinek, and W. Baumeister.
Chapter in Comprehensive Biophysics 1, Biophysical Techniques for Structural Characterization of Macromolecules, ed. E. Egelman, and H.J. Dyson. Elsevier B. V. Academic Press, Oxford, pp. 245-276, 2012.

Structure of the no-go mRNA decay complex Dom34- Hbs1 bound to a stalled 80S ribosome.
T.Becker, J.P. Armache, A.M. Anger, E. Villa, H. Sieber, B.A. Motaal, T. Mielke, O. Berninghausen, and R. Beckmann.
Nat Struct Mol Biol. 18, 715-20, 2011.

Applications of the molecular dynamics flexible fitting method.
L.G. Trabuco, E. Schreiner, J. Gumbart, J. Hsin, E. Villa, and K. Schulten.
Journal of Structural Biology, 173, 420-427, 2011.

Integration of cryo-EM with atomic and protein-protein interaction data.
F. Foerster, E. Villa.
Meth. Enzymol., 483:47-72, 2010.

Localization of eukaryote-specific ribosomal proteins in a 5.5-A cryo-EM map of the 80S eukaryotic ribosome.
 J.P. Armache*, A. Jarasch*, A.M. Anger*, E. Villa, T. Becker, S. Bhushan, F. Jossinet, M. Habeck, G. Dindar, S. Franckenberg, V. Marquez, T. Mielke, M. Thomm, O. Berninghausen, B. Beatrix, J. Soeding, E. Westhof, D.N. Wilson, and R. Beckmann.
PNAS, 107: 19754-19759, 2010.

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. J.P. Armache*, A. Jarasch*, A.M. Anger*, E. Villa, T. Becker, S. Bhushan, F. Jossinet, M. Habeck, G. Dindar, S. Franckenberg, V. Marquez, T. Mielke, M. Thomm, O. Berninghausen, B. Beatrix, J. Soeding, E. Westhof, D.N. Wilson, and R. Beckmann.
PNAS, 107: 19748-19753, 2010.

Visualizing cellular processes at the molecular level by cryo-electron tomography.
K. Ben-Harush, T. Maimon, I. Patla, E. Villa, and O. Medalia.
J. Cell Science, 123:7?12, 2010.

Regulation of the protein–conducting channel by a bound ribosome.
J.Gumbart, L.G.Trabuco, E.Schreiner, E. Villa, and K. Schulten.
Structure, 17:1453-1464, 2009.

Structural insight into nascent polypeptide chain-mediated translational stalling.
B. Seidelt, C.A. Innis, D.N. Wilson, M. Gartmann, J.P. Armache, E. Villa, L.G. Trabuco, T. Becker, T. Mielke, K. Schulten, T.A. Steitz, and R. Beckmann.
Science, 326:1412-1415, 2009.

Protein–induced membrane curvature investigated through molecular dynamics flexible fitting.
J. Hsin, J. Gumbart, L.G. Trabuco, E. Villa, P. Qian, C.N. Hunter, and K. Schulten.
Biophysical Journal, 97:321:329, 2009.

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and x-ray crystallography.
L.G. Trabuco*, EV*, E. Schreiner, C. B. Harrison, and K. Schulten. Methods, 49:174:180, 2009.

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
EV*, J. Sengupta*, L. Trabuco, J. LeBarron, W.T. Baxter, T. Shaikh, R.A. Grassucci, M. Ehrenberg, K. Schulten, and J. Frank.
PNAS 106:1063:1068, 2009.

Structural model and excitonic properties of the dimeric LH1-RC-PufX complex from Rhodobacter sphaeroides.
M.K. Sener, J. Hsin, L.G. Trabuco, E. Villa, P. Qian, P.A. Bullough, C.N. Hunter, and K. Schulten.
Chemical Physics, 357:188-197, 2009.

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics.
L. G. Trabuco*, EV*, K. Mitra, J. Frank, and K. Schulten.
Structure, 16:673-683, 2008.

Molecular mechanisms of cellular mechanics.
M. Gao, M. Sotomayor, E. Villa, E. Lee, and K. Schulten.
Phys. Chem. Chem. Phys., 8:3692?3706, 2006.

Scalable molecular dynamics with NAMD.
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten.
J. Comp. Chem., 26:1781-1802, 2005.

Structural dynamics of the Lac repressor-DNA complex revealed by a multiscale simulation.
E. Villa, A. Balaeff, and K. Schulten.
PNAS, 102:6783-6788, 2005.

Multi-scale method for simulating protein-DNA complexes.
E. Villa, A. Balaeff, L. Mahadevan, and K. Schulten.
Multiscale Modeling and Simulation, 2:527-553, 2004.

*Equal contribution; ‡Co-corresponding author