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Steven Ludtke Lab

Publications

Master
Content

Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. Integrative structure and functional anatomy of a nuclear pore complex. Nature. 2018 Mar 22; 555(7697):475-482. PMID: 29539637. View in: PubMed

Zhang K, Keane SC, Su Z, Irobalieva RN, Chen M, Van V, Sciandra CA, Marchant J, Heng X, Schmid MF, Case DA, Ludtke SJ, Summers MF, Chiu W. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Structure. 2018 Mar 06; 26(3):490-498.e3. PMID: 29398526. View in: PubMed

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. Nat Methods. 2017 Oct; 14(10):983-985. PMID: 28846087. View in: PubMed

Yi P, Wang Z, Feng Q, Chou CK, Pintilie GD, Shen H, Foulds CE, Fan G, Serysheva I, Ludtke SJ, Schmid MF, Hung MC, Chiu W, O'Malley BW. Structural and Functional Impacts of ER Coactivator Sequential Recruitment. Mol Cell. 2017 Sep 07; 67(5):733-743.e4. PMID: 28844863. View in: PubMed

Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. Biophys Rep. 2017; 3(1):17-35. PMID: 28781998. View in: PubMed

Cheng TC, Akey IV, Yuan S, Yu Z, Ludtke SJ, Akey CW. A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation. Structure. 2017 Jan 03; 25(1):40-52. PMID: 27916517. View in: PubMed

Chen M, Baldwin PR, Ludtke SJ, Baker ML. De Novo modeling in cryo-EM density maps with Pathwalking. J Struct Biol. 2016 Dec; 196(3):289-298. PMID: 27436409. View in: PubMed

Ludtke SJ. Single-Particle Refinement and Variability Analysis in EMAN2.1. Methods Enzymol. 2016; 579:159-89. PMID: 27572727. View in: PubMed

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. J Struct Biol. 2016 Jun; 194(3):383-94. PMID: 27016284; PMCID: PMC4846534 [Available on 06/01/17]. View in: PubMed

Bell JM, Chen M, Baldwin PR, Ludtke SJ. High resolution single particle refinement in EMAN2.1. Methods. 2016 May 1; 100:25-34. PMID: 26931650; PMCID: PMC4848122 [Available on 05/01/17]. View in: PubMed

Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM. The Electron Microscopy eXchange (EMX) initiative. J Struct Biol. 2016 May; 194(2):156-63. PMID: 26873784. View in: PubMed

Murray SC, Gillard BK, Ludtke SJ, Pownall HJ. Direct Measurement of the Structure of Reconstituted High-Density Lipoproteins by Cryo-EM. Biophys J. 2016 Feb 23; 110(4):810-6. PMID: 26743047; PMCID: PMC4775836 [Available on 02/23/17]. View in: PubMed

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 Res. 2016 Jan 4; 44(D1):D396-403. PMID: 26578576. View in: PubMed

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. Nat Commun. 2015; 6:8851. PMID: 26511109. View in: PubMed

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. Nat Commun. 2015; 6:8440. PMID: 26455586. View in: PubMed

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 Nov 19; 527(7578):336-41. PMID: 26458101. View in: PubMed

Galaz-Montoya JG, Flanagan J, Schmid MF, Ludtke SJ. Single particle tomography in EMAN2. J Struct Biol. 2015 Jun; 190(3):279-90. PMID: 25956334. View in: PubMed

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. J Struct Biol. 2015 Jun; 190(3):348-59. PMID: 25913484. View in: PubMed

Cheng A, Henderson R, Mastronarde D, Ludtke SJ, Schoenmakers RH, Short J, Marabini R, Dallakyan S, Agard D, Winn M. MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography. J Struct Biol. 2015 Nov; 192(2):146-50. PMID: 25882513. View in: PubMed

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. Mol Cell. 2015 Mar 19; 57(6):1047-58. PMID: 25728767; PMCID: PMC4369429. View in: PubMed

Dai W, Fu C, Khant HA, Ludtke SJ, Schmid MF, Chiu W. Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages. Nat Protoc. 2014 Nov; 9(11):2630-42. PMID: 25321408; PMCID: PMC4371552. View in: PubMed

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. Nat Commun. 2014; 5:4808. PMID: 25185801; PMCID: PMC4155512. View in: PubMed

Chen Z, Fischer ER, Kouiavskaia D, Hansen BT, Ludtke SJ, Bidzhieva B, Makiya M, Agulto L, Purcell RH, Chumakov K. Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor. Proc Natl Acad Sci U S A. 2013 Dec 10; 110(50):20242-7. PMID: 24277851; PMCID: PMC3864303. View in: PubMed

Park E, Ménétret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW. Structure of the SecY channel during initiation of protein translocation. Nature. 2014 Feb 6; 506(7486):102-6. PMID: 24153188; PMCID: PMC3948209. View in: PubMed

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 Oct 31; 502(7473):707-10. PMID: 24107993; PMCID: PMC3984937. View in: PubMed

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; 2:e00710. PMID: 23853712; PMCID: PMC3707056. View in: PubMed

Ludtke SJ, Serysheva II. Single-particle cryo-EM of calcium release channels: structural validation. Curr Opin Struct Biol. 2013 Oct; 23(5):755-62. PMID: 23831288; PMCID: PMC3805725. View in: PubMed

Stoilova-McPhie S, Lynch GC, Ludtke S, Pettitt BM. Domain organization of membrane-bound factor VIII. Biopolymers. 2013 Jul; 99(7):448-59. PMID: 23616213; PMCID: PMC4090243. View in: PubMed

Murray SC, Flanagan J, Popova OB, Chiu W, Ludtke SJ, Serysheva II. Validation of cryo-EM structure of IP?R1 channel. Structure. 2013 Jun 4; 21(6):900-9. PMID: 23707684; PMCID: PMC3696195. View in: PubMed

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 Jun 14; 288(24):17734-44. PMID: 23612981; PMCID: PMC3682573. View in: PubMed

Tolun G, Makhov AM, Ludtke SJ, Griffith JD. Details of ssDNA annealing revealed by an HSV-1 ICP8-ssDNA binary complex. Nucleic Acids Res. 2013 Jun; 41(11):5927-37. PMID: 23605044; PMCID: PMC3675482. View in: PubMed

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 Apr 2; 21(4):604-13. PMID: 23541894; PMCID: PMC3657317. View in: PubMed, PubMed Central

Rees I, Langley E, Chiu W, Ludtke SJ. EMEN2: an object oriented database and electronic lab notebook. Microsc Microanal. 2013 Feb; 19(1):1-10. PMID: 23360752; PMCID: PMC3907281. View in: PubMed

Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ. Data management challenges in three-dimensional EM. Nat Struct Mol Biol. 2012 Dec; 19(12):1203-7. PMID: 23211764; PMCID: PMC4048199. View in: PubMed

Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W. The 2010 cryo-EM modeling challenge. Biopolymers. 2012 Sep; 97(9):651-4. PMID: 22696402. View in: PubMed

Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure. 2012 May 9; 20(5):814-25. PMID: 22503819; PMCID: PMC3350567. View in: PubMed

Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML. Constructing and validating initial C? models from subnanometer resolution density maps with pathwalking. Structure. 2012 Mar 7; 20(3):450-63. PMID: 22405004; PMCID: PMC3307788. View in: PubMed

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 Feb 8; 20(2):205-14. PMID: 22325770; PMCID: PMC3328769. View in: PubMed

Cong Y, Schröder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W. Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. EMBO J. 2012 Feb 1; 31(3):720-30. PMID: 22045336; PMCID: PMC3273382. View in: PubMed

Ludtke SJ, Tran TP, Ngo QT, Moiseenkova-Bell VY, Chiu W, Serysheva II. Flexible architecture of IP3R1 by Cryo-EM. Structure. 2011 Aug 10; 19(8):1192-9. PMID: 21827954; PMCID: PMC3154621. View in: PubMed

Yuan S, Yu X, Asara JM, Heuser JE, Ludtke SJ, Akey CW. The holo-apoptosome: activation of procaspase-9 and interactions with caspase-3. Structure. 2011 Aug 10; 19(8):1084-96. PMID: 21827945; PMCID: PMC3155825. View in: PubMed

Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. Structure of the Drosophila apoptosome at 6.9 å resolution. Structure. 2011 Jan 12; 19(1):128-40. PMID: 21220123; PMCID: PMC3053581. View in: PubMed

Ludtke SJ, Lawson CL, Kleywegt GJ, Berman HM, Chiu W. Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines. Pac Symp Biocomput. 2011; 369-73. PMID: 21121065; PMCID: PMC3617577. View in: PubMed

Baird NJ, Ludtke SJ, Khant H, Chiu W, Pan T, Sosnick TR. Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. J Am Chem Soc. 2010 Nov 24; 132(46):16352-3. PMID: 21038867; PMCID: PMC2988076. View in: PubMed

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 Jan; 39(Database issue):D456-64. PMID: 20935055; PMCID: PMC3013769. View in: PubMed

Baker ML, Zhang J, Ludtke SJ, Chiu W. Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat Protoc. 2010 Sep; 5(10):1697-708. PMID: 20885381; PMCID: PMC3107675. View in: PubMed

Serysheva II, Ludtke SJ. 3D Structure of IP(3) Receptor. Curr Top Membr. 2010; 66:171-89. PMID: 22353480. View in: PubMed

Yuan S, Yu X, Topf M, Ludtke SJ, Wang X, Akey CW. Structure of an apoptosome-procaspase-9 CARD complex. Structure. 2010 May 12; 18(5):571-83. PMID: 20462491; PMCID: PMC2874686. View in: PubMed

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-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci U S A. 2010 Mar 16; 107(11):4967-72. PMID: 20194787; PMCID: PMC2841888. View in: PubMed

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 Jan 21; 463(7279):379-83. PMID: 20090755; PMCID: PMC2834796. View in: PubMed

Cong Y, Ludtke SJ. Single particle analysis at high resolution. Methods Enzymol. 2010; 482:211-35. PMID: 20888963. View in: PubMed

Ludtke SJ. 3-D structures of macromolecules using single-particle analysis in EMAN. Methods Mol Biol. 2010; 673:157-73. PMID: 20835797. View in: PubMed

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 Jan 19; 107(3):1059-64. PMID: 20080547; PMCID: PMC2798884. View in: PubMed

Han M, Mei Y, Khant H, Ludtke SJ. Characterization of antibiotic peptide pores using cryo-EM and comparison to neutron scattering. Biophys J. 2009 Jul 8; 97(1):164-72. PMID: 19580754; PMCID: PMC2711362. View in: PubMed

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 May 13; 17(5):749-58. PMID: 19446530; PMCID: PMC2705691. View in: PubMedl

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 Mar 24; 106(12):4653-8. PMID: 19264960; PMCID: PMC2660777. View in: PubMed

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 Feb 24; 48(7):1481-7. PMID: 19191587; PMCID: PMC2962917. View in: PubMed

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 Jul 15; 105(28):9610-5. PMID: 18621707; PMCID: PMC2474495. View in: PubMed

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 Jul; 15(7):746-53. PMID: 18536725; PMCID: PMC2546500. View in: PubMed

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 Mar; 16(3):441-8. PMID: 18334219. View in: PubMed