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Items: 1 to 50 of 101

1.

MicroED with the Falcon III direct electron detector.

Hattne J, Martynowycz MW, Penczek PA, Gonen T.

IUCrJ. 2019 Aug 17;6(Pt 5):921-926. doi: 10.1107/S2052252519010583. eCollection 2019 Sep 1.

2.

Membrane insertion of α-xenorhabdolysin in near-atomic detail.

Schubert E, Vetter IR, Prumbaum D, Penczek PA, Raunser S.

Elife. 2018 Jul 16;7. pii: e38017. doi: 10.7554/eLife.38017.

3.

3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound.

Brignole EJ, Tsai KL, Chittuluru J, Li H, Aye Y, Penczek PA, Stubbe J, Drennan CL, Asturias F.

Elife. 2018 Feb 20;7. pii: e31502. doi: 10.7554/eLife.31502.

4.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE.

Moriya T, Saur M, Stabrin M, Merino F, Voicu H, Huang Z, Penczek PA, Raunser S, Gatsogiannis C.

J Vis Exp. 2017 May 16;(123). doi: 10.3791/55448.

5.

Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex.

Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H.

Mol Cell. 2016 Oct 20;64(2):236-250. doi: 10.1016/j.molcel.2016.09.009. Epub 2016 Oct 13.

6.

Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy.

Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4017-25. doi: 10.1073/pnas.1500257112. Epub 2015 Jul 13.

7.

Structural snapshots of actively translating human ribosomes.

Behrmann E, Loerke J, Budkevich TV, Yamamoto K, Schmidt A, Penczek PA, Vos MR, Bürger J, Mielke T, Scheerer P, Spahn CM.

Cell. 2015 May 7;161(4):845-57. doi: 10.1016/j.cell.2015.03.052.

8.

A primer to single-particle cryo-electron microscopy.

Cheng Y, Grigorieff N, Penczek PA, Walz T.

Cell. 2015 Apr 23;161(3):438-449. doi: 10.1016/j.cell.2015.03.050. Review.

9.

Structure of the F-actin-tropomyosin complex.

von der Ecken J, Müller M, Lehman W, Manstein DJ, Penczek PA, Raunser S.

Nature. 2015 Mar 5;519(7541):114-7. doi: 10.1038/nature14033. Epub 2014 Dec 1.

10.

Visualization of arrestin recruitment by a G-protein-coupled receptor.

Shukla AK, Westfield GH, Xiao K, Reis RI, Huang LY, Tripathi-Shukla P, Qian J, Li S, Blanc A, Oleskie AN, Dosey AM, Su M, Liang CR, Gu LL, Shan JM, Chen X, Hanna R, Choi M, Yao XJ, Klink BU, Kahsai AW, Sidhu SS, Koide S, Penczek PA, Kossiakoff AA, Woods VL Jr, Kobilka BK, Skiniotis G, Lefkowitz RJ.

Nature. 2014 Aug 14;512(7513):218-222. doi: 10.1038/nature13430. Epub 2014 Jun 22.

11.

Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.

Wu B, Peisley A, Tetrault D, Li Z, Egelman EH, Magor KE, Walz T, Penczek PA, Hur S.

Mol Cell. 2014 Aug 21;55(4):511-23. doi: 10.1016/j.molcel.2014.06.010. Epub 2014 Jul 10.

12.

CTER-rapid estimation of CTF parameters with error assessment.

Penczek PA, Fang J, Li X, Cheng Y, Loerke J, Spahn CM.

Ultramicroscopy. 2014 May;140:9-19. doi: 10.1016/j.ultramic.2014.01.009. Epub 2014 Feb 7.

13.

Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.

Coudray N, Valvo S, Hu M, Lasala R, Kim C, Vink M, Zhou M, Provasi D, Filizola M, Tao J, Fang J, Penczek PA, Ubarretxena-Belandia I, Stokes DL.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2140-5. doi: 10.1073/pnas.1215455110. Epub 2013 Jan 22.

14.

Structure of the rigor actin-tropomyosin-myosin complex.

Behrmann E, Müller M, Penczek PA, Mannherz HG, Manstein DJ, Raunser S.

Cell. 2012 Jul 20;150(2):327-38. doi: 10.1016/j.cell.2012.05.037.

15.

Interaction of the mediator head module with RNA polymerase II.

Cai G, Chaban YL, Imasaki T, Kovacs JA, Calero G, Penczek PA, Takagi Y, Asturias FJ.

Structure. 2012 May 9;20(5):899-910. doi: 10.1016/j.str.2012.02.023.

16.

Arrangement of the respiratory chain complexes in Saccharomyces cerevisiae supercomplex III2IV2 revealed by single particle cryo-electron microscopy.

Mileykovskaya E, Penczek PA, Fang J, Mallampalli VK, Sparagna GC, Dowhan W.

J Biol Chem. 2012 Jun 29;287(27):23095-103. doi: 10.1074/jbc.M112.367888. Epub 2012 May 9.

17.

Iterative stable alignment and clustering of 2D transmission electron microscope images.

Yang Z, Fang J, Chittuluru J, Asturias FJ, Penczek PA.

Structure. 2012 Feb 8;20(2):237-47. doi: 10.1016/j.str.2011.12.007.

18.

Outcome of the first electron microscopy validation task force meeting.

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.

Structure. 2012 Feb 8;20(2):205-14. doi: 10.1016/j.str.2011.12.014.

19.

Real-space processing of helical filaments in SPARX.

Behrmann E, Tao G, Stokes DL, Egelman EH, Raunser S, Penczek PA.

J Struct Biol. 2012 Feb;177(2):302-13. doi: 10.1016/j.jsb.2011.12.020. Epub 2012 Jan 11.

20.

Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images.

Penczek PA, Kimmel M, Spahn CM.

Structure. 2011 Nov 9;19(11):1582-90. doi: 10.1016/j.str.2011.10.003.

21.

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.

Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, Penczek PA, Wilson DN, Spahn CM.

Nature. 2010 Dec 2;468(7324):713-6. doi: 10.1038/nature09547.

22.

Resolution measures in molecular electron microscopy.

Penczek PA.

Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8.

23.

Image restoration in cryo-electron microscopy.

Penczek PA.

Methods Enzymol. 2010;482:35-72. doi: 10.1016/S0076-6879(10)82002-6.

24.

Fundamentals of three-dimensional reconstruction from projections.

Penczek PA.

Methods Enzymol. 2010;482:1-33. doi: 10.1016/S0076-6879(10)82001-4. Review.

25.

Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM.

Spahn CM, Penczek PA.

Curr Opin Struct Biol. 2009 Oct;19(5):623-31. doi: 10.1016/j.sbi.2009.08.001. Epub 2009 Sep 18. Review.

26.

GTPase activation of elongation factor EF-Tu by the ribosome during decoding.

Schuette JC, Murphy FV 4th, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CM.

EMBO J. 2009 Mar 18;28(6):755-65. doi: 10.1038/emboj.2009.26. Epub 2009 Feb 19.

27.

Rubisco in complex with Rubisco large subunit methyltransferase.

Raunser S, Magnani R, Huang Z, Houtz RL, Trievel RC, Penczek PA, Walz T.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3160-5. doi: 10.1073/pnas.0810563106. Epub 2009 Feb 10.

28.

Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.

Zhang W, Kimmel M, Spahn CM, Penczek PA.

Structure. 2008 Dec 10;16(12):1770-6. doi: 10.1016/j.str.2008.10.011.

29.

Cryo-EM image alignment based on nonuniform fast Fourier transform.

Yang Z, Penczek PA.

Ultramicroscopy. 2008 Aug;108(9):959-69. doi: 10.1016/j.ultramic.2008.03.006. Epub 2008 Apr 8.

30.

Structural organization of the anaphase-promoting complex bound to the mitotic activator Slp1.

Ohi MD, Feoktistova A, Ren L, Yip C, Cheng Y, Chen JS, Yoon HJ, Wall JS, Huang Z, Penczek PA, Gould KL, Walz T.

Mol Cell. 2007 Dec 14;28(5):871-85.

31.

Structure of the ribosome-bound cricket paralysis virus IRES RNA.

Schüler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM.

Nat Struct Mol Biol. 2006 Dec;13(12):1092-6. Epub 2006 Nov 19.

PMID:
17115051
32.

SPARX, a new environment for Cryo-EM image processing.

Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams PD, Ludtke SJ.

J Struct Biol. 2007 Jan;157(1):47-55. Epub 2006 Jul 16.

PMID:
16931051
33.

The Transform Class in SPARX and EMAN2.

Baldwin PR, Penczek PA.

J Struct Biol. 2007 Jan;157(1):250-61. Epub 2006 Jun 17.

PMID:
16861004
34.

The parallelization of SPIDER on distributed-memory computers using MPI.

Yang C, Penczek PA, Leith A, Asturias FJ, Ng EG, Glaeser RM, Frank J.

J Struct Biol. 2007 Jan;157(1):240-9. Epub 2006 Jun 8.

PMID:
16859923
35.

The endosome-associated protein Hrs is hexameric and controls cargo sorting as a "master molecule".

Pullan L, Mullapudi S, Huang Z, Baldwin PR, Chin C, Sun W, Tsujimoto S, Kolodziej SJ, Stoops JK, Lee JC, Waxham MN, Bean AJ, Penczek PA.

Structure. 2006 Apr;14(4):661-71.

36.

Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.

Grob P, Cruse MJ, Inouye C, Peris M, Penczek PA, Tjian R, Nogales E.

Structure. 2006 Mar;14(3):511-20.

37.

A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation.

Penczek PA, Frank J, Spahn CM.

J Struct Biol. 2006 May;154(2):184-94. Epub 2006 Feb 17. Review.

PMID:
16520062
38.

Estimation of variance in single-particle reconstruction using the bootstrap technique.

Penczek PA, Yang C, Frank J, Spahn CM.

J Struct Biol. 2006 May;154(2):168-83. Epub 2006 Feb 13.

PMID:
16510296
39.

ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane.

Blau M, Mullapudi S, Becker T, Dudek J, Zimmermann R, Penczek PA, Beckmann R.

Nat Struct Mol Biol. 2005 Nov;12(11):1015-6.

PMID:
16244660
40.

Estimating alignment errors in sets of 2-D images.

Baldwin PR, Penczek PA.

J Struct Biol. 2005 May;150(2):211-25.

PMID:
15866744
41.

Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm.

Yang C, Ng EG, Penczek PA.

J Struct Biol. 2005 Jan;149(1):53-64.

PMID:
15629657
42.

Rearrangement of the 16S precursor subunits is essential for the formation of the active 20S proteasome.

Mullapudi S, Pullan L, Bishop OT, Khalil H, Stoops JK, Beckmann R, Kloetzel PM, Krüger E, Penczek PA.

Biophys J. 2004 Dec;87(6):4098-105. Epub 2004 Sep 10.

43.

Gridding-based direct Fourier inversion of the three-dimensional ray transform.

Penczek PA, Renka R, Schomberg H.

J Opt Soc Am A Opt Image Sci Vis. 2004 Apr;21(4):499-509.

PMID:
15078020
44.

Application of template matching technique to particle detection in electron micrographs.

Huang Z, Penczek PA.

J Struct Biol. 2004 Jan-Feb;145(1-2):29-40.

PMID:
15065671
45.

Automatic particle selection: results of a comparative study.

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.

J Struct Biol. 2004 Jan-Feb;145(1-2):3-14.

PMID:
15065668
46.

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.

Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jørgensen R, Andersen GR, Beckmann R, Penczek PA, Ballesta JP, Frank J.

EMBO J. 2004 Mar 10;23(5):1008-19. Epub 2004 Feb 19.

47.

Automated determination of parameters describing power spectra of micrograph images in electron microscopy.

Huang Z, Baldwin PR, Mullapudi S, Penczek PA.

J Struct Biol. 2003 Oct-Nov;144(1-2):79-94.

PMID:
14643211
48.

Analytical methods and software tools for macromolecular microscopy.

Carragher B, Penczek PA.

J Struct Biol. 2003 Oct-Nov;144(1-2):1-3. No abstract available.

PMID:
14643204
49.
50.

Efficiency of 2D alignment methods.

Joyeux L, Penczek PA.

Ultramicroscopy. 2002 Jul;92(2):33-46.

PMID:
12138941

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