NYSBC - New York Structural Biology Center

SEMC Publications

2017



Wang L, Eng ET, Law K, Gordon RE, Rice WJ, Chen B. Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy. J Virol. 2017 Jan 3;91(2).
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Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure, May 2017;25(3):434-445.
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2016



Cheng A, Tan YZ, Dandey VP, Potter CS, Carragher B. Strategies for Automated CryoEM Data Collection Using Direct Detectors. Methods Enzymol. 2016;579:87-102.
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Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell, 2016;167(6):1610-22 e15.
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Domanski M, Upla P, Rice WJ, Molloy KR, Ketaren NE, Stokes DL, Jensen TH, Rout MP, LaCava J. Purification and analysis of endogenous human RNA exosome complexes. Rna. 2016;22(9):1467-75.
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Fernandez-Martinez J, Kim SJ, Shi Y, Upula P, Pellarin R, Gagnon M. Chemmama IE, Wang J, NudelmanI, Zhang W. Williams R, Rice WJ, Stokes DL, Zenklusen D. Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell. 2016;167(5):1215-1228.e25.
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Haka AS, Barbosa-Lorenzi VC, Lee HJ, Falcone DJ, Hudis CA, Dannenberg AJ, Maxfield FR. Exocytosis of Macrophage Lysosomes Leads to Digestion of Apoptotic Adipocytes and Foam Cell Formation. J Lipid Res. (2016);57(6):980-92.
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Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng Xia L, Korchev YE, Gorelik J, Fenyo D, Rothenberg E, Delmar M. Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc. Nat Commun. 2016;7:10342.
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Peng X, Yuan XZ, Somasundaran P, PatraP. Assessment of micro-polarity anisotrophy as a function of surfactant packing in sodium dodecyl sulphonate-hexane reverse micelles. Soft Matter. 2016;12(1):22-5.
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Razinkov I, Dandey VP, Wei H, Zhang Z, Melnekoff D, Rice WJ, Wigge C, Potter CS, Carragher B. A new method for vitrifying samples for cryoEM. J Struct Biol. 2016;195(2):190-8..
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Singh RK, Barbosa-Lorenzi VC, Lund FW, Grosheva I, Maxfield FR, Haka AS. Degradation of aggregated LDL occurs in complex extracellular sub-compartments of the lysosomal synapse. J Cell Sci.2016;129(5):1072-82.
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Singhvi A, Liu B, Friedman CJ, Fong J, Lu Y, Huang XY, Shaham S. A Glial K/Cl Transporter Controls Neuronal Receptive Ending Shape by Chloride Inhibition of an rGC. Cell. 2016;165(4):936-48.
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Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf). 2016;65(1):43-56.
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2015



(2015). Correction for Kaushal et al., Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A. 2015;112(20):E2736.
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Chuang JZ, Hsu YC, Sung CH. Ultrastructural visualization of trans-ciliary rhodopsin cargoes in mammalian rods. Cilia. 2015;4:4.
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Hall DH, Rice WJ. Electron Tomography Methods for C. elegans. Methods Mol Biol. 2015;1327:141-58.
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Hsu YC, Chuang JZ, Sung CH. Light regulates the ciliary protein transport and outer segment disc renewal of mammalian photoreceptors. Developmental Cell. 2015;32(6):731-742.
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Hurd TR, Sanchez CG, Teixeira FK, Petzold C, Dancel-Manning K, Wang JY, Lehmann R, Liang FX. Ultrastructural Analysis of Drosophila Ovaries by Electron Microscopy. Methods Mol Biol. 2015;1328:151-62.
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Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MH, Zhang C, Moeller A, West GM, Pascal BD, Van Eps N, Caro LN, Vishnivetskiy SA, Lee RJ, Suino-Powell KM, Gu X, Pal K, Ma J, Zhi X, Boutet S, Williams GJ, Messerschmidt M, Gati C, Zatsepin NA, Wang D, James D, Basu S, Roy-Chowdhury S, Conrad CE, Coe J, Liu H, Lisova S, Kupitz C, Grotjohann I, Fromme R, Jiang Y, Tan M, Yang H, Li J, Wang M, Zheng Z, Li D, Howe N, Zhao Y, Standfuss J, Diederichs K, Dong Y, Potter CS, Carragher B, Caffrey M, Jiang H, Chapman HN, Spence JC, Fromme P, Weierstall U, Ernst OP, Katritch V, Gurevich VV, Griffin PR, Hubbell WL, Stevens RC, Cherezov V, Melcher K, Xu HE. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature. 2015;523(7562):561-7.
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Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai A, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Journal of structural biology. 2015;189(2):123-134.
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Leo-Macias A, Liang FX, Delmar M. Ultrastructure of the intercellular space in adult murine ventricle revealed by quantitative tomographic electron microscopy. Cardiovasc Res. 2015;107(4):442-452.
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Neel BA, Zong H, Backer JM, Pessin JE, Identification of Atypical Peri-Nuclear Multivesicular Bodies in Oxidative and Glycolytic Skeletal Muscle of Aged and Pompe's Disease Mouse Models. Frontiers in Physiology. 2015;6:393.
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Totland C, Martinez-Santiago J, Ananthapadmanabhan KP, Somasundaran P. Composition and structural transitions of polyelectrolyte-surfactant complexes in the presence of fatty acid studied by NMR and cryo-SEM. Langmuir:the ACS journal of surfaces and colloids. 2015;31(5):1623-1631.
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2014



Block, K. A., et al., Disassembly of the cystovirus varphi6 envelope by montmorillonite clay. Microbiologyopen 3(1): 42-51.
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Choudhuri, K., et al., Polarized release of T-cell-receptor-enriched microvesicles at the immunological synapse. Nature 507(7490): 118-123. Show/Hide Abstract
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Fu, X, et al., Controlled bacterial lysis for electron tomography of native cell membranes. Structure 22(12): 1875-1882. Show/Hide Abstract
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Katz, G, et al., Morphology of influenza B/Lee/40 determined by cryo-electron microscopy. PLoS One 9(2): e88288. Show/Hide Abstract
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Kaushal, PS, et al., Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A 111(20): 7284-7289. Show/Hide Abstract
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Nguyen, PA, et al., Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans thermosensory neuron. J Cell Sci 127(24): 5317-5330. Show/Hide Abstract
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Orlando, BJ, et al., Cyclooxygenase-2 catalysis and inhibition in lipid bilayer nanodiscs. Arch Biochem Biophys 546: 33-40. Show/Hide Abstract
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Wang, J, et al., C. elegans ciliated sensory neurons release extracellular vesicles that function in animal communication. Curr Biol 24(5): 519-525. Show/Hide Abstract
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Yakubovskaya, E, et al., Organization of the human mitochondrial transcription initiation complex. Nucleic Acids Res 42(6): 4100-4112. Show/Hide Abstract
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2013



Allen, GS and DL Stokes, Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy. Methods Mol Biol 955: 229-241. Show/Hide Abstract

Asenjo, AB, et al., Structural model for tubulin recognition and deformation by kinesin-13 microtubule depolymerases. Cell Rep 3(3): 759-768. Show/Hide Abstract

Catanese, MT, et al., Ultrastructural analysis of hepatitis C virus particles. Proc Natl Acad Sci U S A 110(23): 9505-9510. Show/Hide Abstract

Choi, WS, et al., Three-dimensional reconstruction of intact human integrin alphaIIbbeta3: new implications for activation-dependent ligand binding. Blood 122(26): 4165-4171. Show/Hide Abstract

Coudray, N, et al., Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy. Proc Natl Acad Sci U S A 110(6): 2140-2145. Show/Hide Abstract

Khan, LA, et al., Intracellular lumen extension requires ERM-1-dependent apical membrane expansion and AQP-8-mediated flux. Nat Cell Biol 15(2): 143-156. Show/Hide Abstract

Pieper, U, et al., Coordinating the impact of structural genomics on the human alpha-helical transmembrane proteome. Nat Struct Mol Biol 20(2): 135-138. Show/Hide Abstract

Sampathkumar, P, et al., Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure 21(4): 560-571. Show/Hide Abstract

Stokes, DL, et al., High-throughput methods for electron crystallography. Methods Mol Biol 955: 273-296. Show/Hide Abstract

Yang, S, et al., Molecular mechanism of fascin function in filopodial formation. J Biol Chem 288(1): 274-284. Show/Hide Abstract

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2012



Cerrone, M, et al., "Sodium current deficit and arrhythmogenesis in a murine model of plakophilin-2 haploinsufficiency." Cardiovasc Res 95(4): 460-468. Show/Hide Abstract

Delmar, M and Liang, FX, Connexin43 and the regulation of intercalated disc function. Heart Rhythm 9(5): 835-838. Show/Hide Abstract

Durand-Heredia, J, et al., Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli. J Bacteriol 194(12): 3189-3198. Show/Hide Abstract

Fernandez-Martinez, J, et al., Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol 196(4): 419-434. Show/Hide Abstract

Hom, N, et al., Anisotropic nanocrystal arrays organized on protein lattices formed by recombinant clathrin fragments. J Mater Chem 22(44): 23335-23339. Show/Hide Abstract

Katz, G, et al., Protein P7 of the cystovirus phi6 is located at the three-fold axis of the unexpanded procapsid. PLoS One 7(10): e47489. Show/Hide Abstract

Phoon, CK, et al., Tafazzin knockdown in mice leads to a developmental cardiomyopathy with early diastolic dysfunction preceding myocardial noncompaction. J Am Heart Assoc 1(2). Show/Hide Abstract

Schlame, M, et al., The physical state of lipid substrates provides transacylation specificity for tafazzin. Nat Chem Biol 8(10): 862-869. Show/Hide Abstract

Topalidou, I, et al., Genetically separable functions of the MEC-17 tubulin acetyltransferase affect microtubule organization. Curr Biol 22(12): 1057-1065. Show/Hide Abstract

Topalidou, I, et al., Enzymatic and non-enzymatic activities of the tubulin acetyltransferase MEC-17 are required for microtubule organization and mechanosensation in C. elegans. Current Biology 22(12): 1057-1065. Show/Hide Abstract

Ubarretxena-Belandia, I and Stokes, DL (2012), Membrane protein structure determination by electron crystallography. Curr Opin Struct Biol 22(4): 520-528. Show/Hide Abstract

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2011



Acehan, D, et al., Cardiolipin affects the supramolecular organization of ATP synthase in mitochondria. Biophys J 100(9): 2184-2192. Show/Hide Abstract

Allen, GS, et al., The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. Structure 19(9): 1219-1232. Show/Hide Abstract

Banerjee, S and Nimigean, CM, Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers. J Gen Physiol 137(2): 217-223. Show/Hide Abstract

De Carlo, S and Harris, JR, Negative staining and cryo-negative staining of macromolecules and viruses for TEM. Micron 42(2): 117-131. Show/Hide Abstract

Durand-Heredia, JM., et al., Identification and characterization of ZapC, a stabilizer of the FtsZ ring in Escherichia coli. J Bacteriol 193(6): 1405-1413. Show/Hide Abstract

Leo-Macias, A, et al., Toroidal surface complexes of bacteriophage ?12 are responsible for host-cell attachment. Virology 414(2): 103-109. Show/Hide Abstract

Nans, A, et al., Electron tomography of paranodal septate-like junctions and the associated axonal and glial cytoskeletons in the central nervous system. J Neurosci Res 89(3): 310-319. TShow/Hide Abstract

Nans, A, et al., Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography. Biophys J 101(10): 2341-2350. Show/Hide Abstract

Renzi, F, et al., Structure of gamma-secretase and its trimeric pre-activation intermediate by single-particle electron microscopy. J Biol Chem 286(24): 21440-21449. Show/Hide Abstract

Tian, Y, et al., Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex. Nat Struct Mol Biol 18(6): 658-664. Show/Hide Abstract

Wehman, AM, et al., The P4-ATPase TAT-5 inhibits the budding of extracellular vesicles in C. elegans embryos. Curr Biol 21(23): 1951-1959. Show/Hide Abstract

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2010



Diaz, R, et al., Fourier-Bessel reconstruction of helical assemblies. Methods Enzymol 482: 131-165. Show/Hide Abstract

Filimonenko, M, et al., The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell 38(2): 265-279. Show/Hide Abstract

Hu, M, et al., Automated electron microscopy for evaluating two-dimensional crystallization of membrane proteins. J Struct Biol 171(1): 102-110. Show/Hide Abstract

Ji, H, et al., Protein determinants of SNARE-mediated lipid mixing. Biophys J 99(2): 553-560. Show/Hide Abstract

Kim, C, et al., An automated pipeline to screen membrane protein 2D crystallization. J Struct Funct Genomics 11(2): 155-166. Show/Hide Abstract

Leal-Pinto, E, et al., Gating of a G protein-sensitive mammalian Kir3.1 prokaryotic Kir channel chimera in planar lipid bilayers. J Biol Chem 285(51): 39790-39800. Show/Hide Abstract

Li, G, et al., Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Mol Cell 38(1): 41-53. Show/Hide Abstract

Melcher, M, et al., Identification of a role for the PfEMP1 semi-conserved head structure in protein trafficking to the surface of Plasmodium falciparum infected red blood cells. Cell Microbiol 12(10): 1446-1462. Show/Hide Abstract

Opalka, N, et al., Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 8(9). Show/Hide Abstract

Owen, GR and Stokes, DL, Exploring the Nature of Desmosomal Cadherin Associations in 3D. Dermatology Research and Practice 2010. Show/Hide Abstract

Stokes, DL, et al., Two-dimensional crystallization of integral membrane proteins for electron crystallography. Methods Mol Biol 654: 187-205. Show/Hide Abstract

Tucker, JD, et al., Membrane invagination in Rhodobacter sphaeroides is initiated at curved regions of the cytoplasmic membrane, then forms both budded and fully detached spherical vesicles. Mol Microbiol 76(4): 833-847. Show/Hide Abstract

Ubarretxena-Belandia, I and Stokes, DL, Present and future of membrane protein structure determination by electron crystallography. Adv Protein Chem Struct Biol 81: 33-60. Show/Hide Abstract

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2009



Acehan, D, et al., Distinct effects of tafazzin deletion in differentiated and undifferentiated mitochondria. Mitochondrion 9(2): 86-95. Show/Hide Abstract

Haka, AS, et al., Macrophages create an acidic extracellular hydrolytic compartment to digest aggregated lipoproteins. Mol Biol Cell 20(23): 4932-4940. Show/Hide Abstract

Jeong, H, et al., Acetylation targets mutant huntingtin to autophagosomes for degradation. Cell 137(1): 60-72. Show/Hide Abstract

Kampmann, M and Blobel, G, Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat Struct Mol Biol 16(7): 782-788. Show/Hide Abstract

Mansilla-Soto, J, et al., DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68. PLoS Pathog 5(7): e1000513. Show/Hide Abstract

Nagy, V, et al., Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Proc Natl Acad Sci U S A 106(42): 17693-17698. Show/Hide Abstract

Rath, U, et al., The Drosophila kinesin-13, KLP59D, impacts Pacman- and Flux-based chromosome movement. Mol Biol Cell 20(22): 4696-4705. Show/Hide Abstract

Shi, Y, et al., Molecular architecture of the human pre-mRNA 3' processing complex. Mol Cell 33(3): 365-376. Show/Hide Abstract

Wei, H, et al., Three-dimensional structure of the enveloped bacteriophage phi12: an incomplete T = 13 lattice is superposed on an enclosed T = 1 shell. PLoS One 4(9): e6850. Show/Hide Abstract

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2008



Acehan, D, et al., Plakoglobin is required for effective intermediate filament anchorage to desmosomes. J Invest Dermatol 128(11): 2665-2675. Show/Hide Abstract

Banerjee, S, et al., Rapid incorporation of functional rhodopsin into nanoscale apolipoprotein bound bilayer (NABB) particles. J Mol Biol 377(4): 1067-1081. Show/Hide Abstract

Eryilmaz, E, et al., Structure and dynamics of the P7 protein from the bacteriophage phi 12. J Mol Biol 382(2): 402-422. Show/Hide Abstract

Georgescu, RE, et al., Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc Natl Acad Sci U S A 105(32): 11116-11121. Show/Hide Abstract

Hu, GB, et al., Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals. J Struct Biol 161(3): 411-418. Show/Hide Abstract

Hu, GB, et al., Electron cryo-tomographic structure of cystovirus phi 12. Virology 372(1): 1-9. Show/Hide Abstract

Milstein, O, et al., Nanoscale increases in CD2-CD48-mediated intermembrane spacing decrease adhesion and reorganize the immunological synapse. J Biol Chem 283(49): 34414-34422. Show/Hide Abstract

Owen, GR, et al., Cryoelectron tomography of isolated desmosomes. Biochem Soc Trans 36(Pt 2): 173-179. Show/Hide Abstract

Tan, D, et al., Structure of the kinesin13-microtubule ring complex. Structure 16(11): 1732-1739. Show/Hide Abstract

Tareste, D, et al., SNAREpin/Munc18 promotes adhesion and fusion of large vesicles to giant membranes. Proc Natl Acad Sci U S A 105(7): 2380-2385. Show/Hide Abstract

Wu, CC, et al., Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure 16(6): 976-985. Show/Hide Abstract

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2007



Acehan, D, et al., Comparison of lymphoblast mitochondria from normal subjects and patients with Barth syndrome using electron microscopic tomography. Lab Invest 87(1): 40-48. Show/Hide Abstract

Chuang, CF, et al., An innexin-dependent cell network establishes left-right neuronal asymmetry in C. elegans. Cell 129(4): 787-799. Show/Hide Abstract

Del Rio, A, et al., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. Journal of Molecular Biology 365(1): 109-122. Show/Hide Abstract

Pomfret, AJ, et al., Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases. J Struct Biol 157(1): 106-116. Show/Hide Abstract

Shen, J, et al., Selective activation of cognate SNAREpins by Sec1/Munc18 proteins. Cell 128(1): 183-195. Show/Hide Abstract

Stokes, DL, Desmosomes from a structural perspective. Curr Opin Cell Biol 19(5): 565-571. Show/Hide Abstract

Vanamee, ES, et al., An EM view of the FokI synaptic complex by single particle analysis. J Mol Biol 370(2): 207-212. Show/Hide Abstract

Vink, M, et al., A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J Struct Biol 160(3): 295-304. Show/Hide Abstract

Yakubovskaya, E, et al., The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. Embo j 26(19): 4283-4291. Show/Hide Abstract

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2006



Barré, P and Eliezer, D, Folding of the Repeat Domain of Tau Upon Binding to Lipid Surfaces. Journal of Molecular Biology 362(2): 312-326. Show/Hide Abstract

Chen, Z, et al., Cross-linking of C-terminal residues of phospholamban to the Ca2+ pump of cardiac sarcoplasmic reticulum to probe spatial and functional interactions within the transmembrane domain. J Biol Chem 281(20): 14163-14172. Show/Hide Abstract

Ferguson, N, et al., General structural motifs of amyloid protofilaments. Proc Natl Acad Sci U S A 103(44): 16248-16253. Show/Hide Abstract

Greig, SL, et al., Structural determinants of rotavirus subgroup specificity mapped by cryo-electron microscopy. J Mol Biol 356(1): 209-221. Show/Hide Abstract

Rice, WJ, et al., Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus. Biochem Biophys Res Commun 348(1): 124-131. Show/Hide Abstract

Stokes, DL, et al., Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals. Biophys J 90(11): 4213-4223. Show/Hide Abstract

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2005



Alimova, A, et al., Virus particles and receptor interaction monitored by fluorescence spectroscopy. Photochem Photobiol 81(4): 879-883. Show/Hide Abstract

Eliezer, D, et al., Residual structure in the repeat domain of tau: echoes of microtubule binding and paired helical filament formation. Biochemistry 44(3): 1026-1036. Show/Hide Abstract

Stokes, DL, et al., Structural studies of a stabilized phosphoenzyme intermediate of Ca2+-ATPase. J Biol Chem 280(18): 18063-18072. Show/Hide Abstract

Wood, MA, et al., Utilizing atomic number contrast for FESEM imaging of colloidal nanotopography underlying biological cells. Nanotechnology 16(9): 1433. Show/Hide Abstract

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2003



He, W, et al., Untangling desmosomal knots with electron tomography. Science 302(5642): 109-113. Show/Hide Abstract

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