Publications

Chen, M, Dai, W, Sun, SY, Jonasch, D, He, CY, Schmid, MF, Chiu, W, & Ludtke, SJ, Convolutional neural networks for automated annotation of cellular cryo-electron tomograms, Nature Methods, 2017

Jesus G. Galaz-Montoya, Steven J. Ludtke, The advent of structural biology in situ by single particle cryo-electron tomography, Biophys, 2017, Rep. doi:10.1007/s41048-017-0040-0

Wang, Z, Fan, G, Hryc, CF, Blaza, JN, Serysheva, II, Schmid, MF, Chiu, W, Luisi, BF, & Du, D, An allosteric transport mechanism for the AcrAB-1 TolC Multidrug Efflux Pump., ELife, 2017, PMCID5404916

Ludtke, SJ, Single-Particle Refinement and Variability Analysis in EMAN2.1, Methods Enzymol, 2016, 579:159-189. PMID27572727

Bell, JM, Chen, M, Baldwin, PR, & Ludtke, SJ, High resolution single particle refinement in EMAN2.1, Methods, 2016, 100:25-34. PMIDPMC4848122

Chen, M, Baldwin, PR, Ludtke, SJ, & Baker, ML, De Novo Modeling in Cryo-EM Density Maps with Pathwalking., J Struct Bio., 2016, PMID27436409

Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevin JM, Patwardhan A, Heymann JB, & Carazo JM, The Electron Microscopy eXchange (EMX) initiative., Journal of structural biology, 2016, 194(2):156-163.

Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, & Chiu W, EMDataBank unified data resource for 3DEM., Nucleic acids research,2016, 44(D1):D396-403. PMCID4702818

Galaz-Montoya,JG, Hecksel,CW, Baldwin,PR, Wang,E, Weaver,SC, Schmid,MF, Ludtke,SJ, & Chiu W, Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography., Journal of structural biology, 2016, 194(3):383-394. PMCID4846534.

Irobalieva, RN, Fogg, JM, Catanese, DJ, Sutthibutpong, T, Chen, M, Barker, AK, Ludtke, SJ, Harris, SA, Schmid, MF, Chiu, W, & Zechiedrich, L, Structural diversity of supercoiled DNA., Nature communications, 2015, 6:8440. PMCID4608029

Irobalieva, RN, Fogg, JM, Catanese, DJ, Sutthibutpong, T, Chen, M, Barker, AK, Ludtke, SJ, Harris, SA, Schmid, MF, Chiu, W, & Zechiedrich, L, Erratum: Structural diversity of supercoiled DNA., Nature communications, 2015, 6:8440. PMID: 26511109

Fan, G, Baker, ML, Wang, Z, Baker, MR, Sinyagovskiy, PA, Chiu, W, Ludtke, SJ, & Serysheva, II, Gating machinery of InsP3R channels revealed by electron cryomicroscopy., Nature, 2015, 527(7578):336-341.

Galaz-Montoya JG, Flanagan J, Schmid MF, Ludtke SJ., Single particle tomography in EMAN2., J Struct Biol., 2015, Jun;190(3):279-90. doi: 10.1016/j.jsb.2015.04.016. Epub 2015 May 5

Marabini, R, Carragher, B, Chen, S, Chen, J, Cheng, A, Downing, KH, Frank, J, Grassucci, RA, Bernard Heymann, J, Jiang, W, Jonic, S, Liao, HY, Ludtke, SJ, Patwari, S, Piotrowski, AL, Quintana, A, Sorzano, CO, Stahlberg, H, Vargas, J, Voss, NR, Chiu, W, & Carazo, JM, CTF Challenge: Result summary, Journal of structural biology, 2015, 10.1016/j.jsb.2015.04.003.

Yi, P, Wang, Z, Feng, Q, Pintilie, GD, Foulds, CE, Lanz, RB, Ludtke, SJ, Schmid, MF, Chiu, W, & O'Malley, BW, Structure of a biologically active estrogen receptor-coactivator complex on DNA., Molecular cell, 2015, 57(6):1047-1058.

Wang, Z, Hryc, CF, Bammes, B, Afonine, PV, Jakana, J, Chen, DH, Liu, X, Baker, ML, Kao, C, Ludtke, SJ, Schmid, MF, Adams, PD, & Chiu, W, An atomic model of brome mosaic virus using direct electron detection and real-space optimization., Nature Communications, 2014

Dai, W, Fu, C, Khant, HA, Ludtke, SJ, Schmid, MF and Chiu, W, Zernike phase contrast electron cryo-tomography applied to marine cyanobacteria Infected with cyanophages., Nature Protocols, 2014

Dai W, Fu C, Raytcheva D, Flanagan J, Khant HA, Liu X, Rochat RH, Haase-Pettingell C, Piret J, Ludtke SJ, Nagayama K, Schmid MF, King JA, Chiu W, Visualizing virus assembly intermediates inside marine cyanobacteria., Nature, 2013

Ludtke SJ, Serysheva II, Single-particle cryo-EM of calcium release channels: structural validation., Curr Opin Struct Biol, 2013

Murray SC, Flanagan J, Popova OB, Chiu W, Ludtke SJ, Serysheva II, Validation of cryo-EM structure of IP₃R1 channel., Structure, 2013

Sergeeva OA, Chen B, Haase-Pettingell C, Ludtke SJ, Chiu W, King JA, Human CCT4 and CCT5 chaperonin subunits expressed in Escherichia coli form biologically active homo-oligomers., J Biol Chem, 2013

Rees I, Langley E, Chiu W, Ludtke SJ, EMEN2: an object oriented database and electronic lab notebook., Microsc Microanal, 2013

Zhang Q, Dai X, Cong Y, Zhang J, Chen DH, Dougherty MT, Wang J, Ludtke SJ, Schmid MF, Chiu W, Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism., Structure, 2013

Shahmoradian SH, Galaz-Montoya JG, Schmid MF, Cong Y, Ma B, Spiess C, Frydman J, Ludtke SJ, Chiu W, TRiC's tricks inhibit huntingtin aggregation., Elife, 2013

Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W, The 2010 cryo-EM modeling challenge., Biopolymers, 2012

Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke SJ, Chiu W, Hartl FU, Aebersold R, Frydman J, The molecular architecture of the eukaryotic chaperonin TRiC/CCT., Structure, 2012

Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML, Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking., Structure, 2012

Ni P, Wang Z, Ma X, Das NC, Sokol P, Chiu W, Dragnea B, Hagan M, Kao CC, An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs., J Mol Biol, 2012

Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL, Outcome of the first electron microscopy validation task force meeting., Structure, 2012

Cong Y, Schröder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SJ, Frydman J, Chiu W, Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. EMBO J, 2012

Kostyuchenko VA, Jakana J, Liu X, Haddow AD, Aung M, Weaver SC, Chiu W, Lok SM, The structure of barmah forest virus as revealed by cryo-electron microscopy at a 6-angstrom resolution has detailed transmembrane protein architecture and interactions., J Virol, 2011

Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W, EMDataBank.org: unified data resource for CryoEM., Nucleic Acids Res, 2011

Ludtke SJ, Tran TP, Ngo QT, Moiseenkova-Bell VY, Chiu W, Serysheva II, Flexible architecture of IP3R1 by Cryo-EM., Structure, 2011

Baker ML, Zhang J, Ludtke SJ, Chiu W, Cryo-EM of macromolecular assemblies at near-atomic resolution., Nat Protoc, 2010

Cong Y, Baker ML, Jakana J, Woolford D, Miller EJ, Reissmann S, Kumar RN, Redding-Johanson AM, Batth TS, Mukhopadhyay A, Ludtke SJ, Frydman J, Chiu W, 4.0-Å resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement., Proc Natl Acad Sci U S A, 2010

Zhang J, Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W, Mechanism of folding chamber closure in a group II chaperonin., Nature, 2010

Ren G, Rudenko G, Ludtke SJ, Deisenhofer J, Chiu W, Pownall HJ, Model of human low-density lipoprotein and bound receptor based on cryoEM., Proc Natl Acad Sci U S A, 2010

Cong Y, Zhang Q, Woolford D, Schweikardt T, Khant H, Dougherty M, Ludtke SJ, Chiu W, Decker H, Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy., Structure, 2009

Zhang R, Hu X, Khant H, Ludtke SJ, Chiu W, Schmid MF, Frieden C, Lee JM, Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM., Proc Natl Acad Sci U S A, 2009

Han M, Mei Y, Khant H, Ludtke SJ, Characterization of antibiotic peptide pores using cryo-EM and comparison to neutron scattering., Biophys J, 2009

Han M, Gillard BK, Courtney HS, Ward K, Rosales C, Khant H, Ludtke SJ, Pownall HJ, Disruption of human plasma high-density lipoproteins by streptococcal serum opacity factor requires labile apolipoprotein A-I., Biochemistry, 2009

Ludtke SJ, Baker ML, Chen DH, Song JL, Chuang DT, Chiu W, De novo backbone trace of GroEL from single particle electron cryomicroscopy., Structure, 2008

Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W, Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel., Proc Natl Acad Sci U S A, 2008

Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J, Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT., Nat Struct Mol Biol,2008

Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams PD, Ludtke SJ, SPARX, a new environment for Cryo-EM image processing., J Struct Biol, 2007

Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ, EMAN2: an extensible image processing suite for electron microscopy., J Struct Biol, 2007

Ménétret JF, Schaletzky J, Clemons WM Jr, Osborne AR, Skånland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW, Ribosome binding of a single copy of the SecY complex: implications for protein translocation., Mol Cell, 2007

Serysheva II, Chiu W, Ludtke SJ, Single-particle electron cryomicroscopy of the ion channels in the excitation-contraction coupling junction., Methods Cell Biol, 2007

Chen DH, Song JL, Chuang DT, Chiu W, Ludtke SJ, An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate., Structure, 2006

Jiang X, Jayaram H, Kumar M, Ludtke SJ, Estes MK, Prasad BV,Cryoelectron microscopy structures of rotavirus NSP2-NSP5 and NSP2-RNA complexes: implications for genome replication., J Virol, 2006

Araç D, Chen X, Khant HA, Ubach J, Ludtke SJ, Kikkawa M, Johnson AE, Chiu W, Südhof TC, Rizo J, Close membrane-membrane proximity induced by Ca(2+)-dependent multivalent binding of synaptotagmin-1 to phospholipids., Nat Struct Mol Biol, 2006

Jiang W, Ludtke SJ, Electron cryomicroscopy of single particles at subnanometer resolution., Curr Opin Struct Biol, 2005

Yu X, Acehan D, Ménétret JF, Booth CR, Ludtke SJ, Riedl SJ, Shi Y, Wang X, Akey CW, A structure of the human apoptosome at 12.8 Å resolution provides insights into this cell death platform., Structure, 2005

Serysheva II, Hamilton SL, Chiu W, Ludtke SJ, Structure of Ca2+ release channel at 14 A resolution., J Mol Biol, 2005

Passmore LA, Booth CR, Vénien-Bryan C, Ludtke SJ, Fioretto C, Johnson LN, Chiu W, Barford D, Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation., Mol Cell, 2005

Sitharaman B, Kissell KR, Hartman KB, Tran LA, Baikalov A, Rusakova I, Sun Y, Khant HA, Ludtke SJ, Chiu W, Laus S, Tóth E, Helm L, Merbach AE, Wilson LJ, Superparamagnetic gadonanotubes are high-performance MRI contrast agents., Chem Commun (Camb), 2005

Ludtke SJ, Serysheva II, Hamilton SL, Chiu W, The pore structure of the closed RyR1 channel., Structure, 2005

Ménétret JF, Hegde RS, Heinrich SU, Chandramouli P, Ludtke SJ, Rapoport TA, Akey CW, Architecture of the ribosome-channel complex derived from native membranes., J Mol Biol, 2005

Chen C, Ko Y, Delannoy M, Ludtke SJ, Chiu W, Pedersen PL, Mitochondrial ATP synthasome: three-dimensional structure by electron microscopy of the ATP synthase in complex formation with carriers for Pi and ADP/ATP., J Biol Chem, 2004

Ludtke SJ, Chen DH, Song JL, Chuang DT, Chiu W, Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy., Structure, 2004

Zhu Y, Carragher B, Glaeser RM, Fellmann D, Bajaj C, Bern M, Mouche F, de Haas F, Hall RJ, Kriegman DJ, Ludtke SJ, Mallick SP, Penczek PA, Roseman AM, Sigworth FJ, Volkmann N, Potter CS., Automatic particle selection: results of a comparative study., J Struct Biol, 2004

Brink J, Ludtke SJ, Kong Y, Wakil SJ, Ma J, Chiu W., Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis., Structure, 2004

Mao Y, Vyas NK, Vyas MN, Chen DH, Ludtke SJ, Chiu W, Quiocho FA., Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer., EMBO J, 2004

Booth CR, Jiang W, Baker ML, Zhou ZH, Ludtke SJ, Chiu W., A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope., J Struct Biol, 2004

Serysheva, I.I, Bare, D.J., Ludtke, S.J., Kettlun, C.S., Chiu, W., and Mignery, G.A., Structure of the type 1 Inositol 1,4,5-trisphosphate receptor revealed by electron cryomicroscopy., J Biol Chem, 2003, 278: 21319-21322.

Ludtke, SJ., Nason, L., Tu, H., Peng, L., and Chiu, W., Object oriented database and electronic notebook for transmission electron microscopy., Microscopy and Microanalysis 2003, 9: 556-565.

Ludtke, SJ. and Chiu, W., Focal pair merging for contrast enhancement of single particles., J Struct Biol, 2003, 144: 73-78.

Brink, J., Ludtke, SJ., Yang, C. Y., Gu, Z. W., Wakil, S. J., and Chiu, W., Quaternary structure of human fatty acid synthase by electron cryomicroscopy., Proc Natl Acad Sci USA, 2002, 99: 138-143.

Serysheva, I.I., Ludtke, SJ., Baker, M. R., Chiu, W., and Hamilton, S. L., Structure of the voltage-gated L-type Ca2+ channel by electron cryomicroscopy., Proc Natl Acad Sci USA, 2002, 99: 10370-10375.

Baker, M. L., Serysheva, I. I., Sencer, S., Wu, Y., Ludtke, SJ., Jiang, W., Hamilton, S. L., and Chiu, W., The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain., Proc Natl Acad Sci USA, 2002, 99: 12155-12160.

Ludtke, S.J., Jakana, J., Song, J.L., Chuang, D., and Chiu, W., A 11.5 Å single particle reconstruction of GroEL using EMAN., J Mol Biol,, 2001, 314: 253-262.

Jiang, W., Baker, M. L., Ludtke, S. J., and Chiu, W., Bridging the information gap: Computational tools for intermediate resolution structure interpretation., J Mol Biol, 2001, 308:1033-1044.

Saad, A., Ludtke, S. J., Jakana, J., Rixon, F. J., Tsuruta, H., and Chiu, W., Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination., J Struct Biol, 2001, 133: 32-42.

Ludtke, S. J. and Chiu, W., Electron micrographs: computer enhancement and use for molecular 3-dimensional reconstruction., In: Encyclopedia of Life Sciences, 2001, vol. 6, pp. 212-217. London: Nature Publishing Group. http://www.els.net/

Ludtke, S. J. and Chiu, W., Editorial comments on special issue on single particle analysis., J Struct Biol, 2001, 133: 89.