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Newsletter Archive  |  Facility News Archive

Manuals:

 

Publications:

Acknowledging the CEMF (for full list click here)

  • Lu, D., Shang, G., He, X., Bai, X.-C., & Zhang, X. (2021). Architecture of the sema3a/plexina4/neuropilin tripartite complex. Nature Communications , 12(1), 3172. PMID 34039996

  • Uchikawa, E., Chen, Z., Xiao, G.-Y., Zhang, X., & Bai, X.-C. (2021). Structural basis of the activation of c-MET receptor. Nature Communications,  12(1), 4074. PMID 34210960

  • Kober, D. L., Radhakrishnan, A., Goldstein, J. L., Brown, M. S., Clark, L. D., Bai, X.-C., & Rosenbaum, D. M. (2021). Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing.  Cell , 184(14), 3689-3701.e22. PMID 34139175

  • Noviello, Colleen M., Anant Gharpure, Nuriya Mukhtasimova, Rico Cabuco, Leah Baxter, Dominika Borek, Steven M. Sine, and Ryan E. Hibbs. “Structure and Gating Mechanism of the Α7 Nicotinic Acetylcholine Receptor.”  Cell  184, no. 8 (April 15, 2021): 2121-2134.e13. PMID 33735609

  • Jeong, Byung-Cheon, Sung Jun Bae, Lisheng Ni, Xuewu Zhang, Xiao-Chen Bai, and Xuelian Luo. “Cryo-EM Structure of the Hippo Signaling Integrator Human STRIPAK.” Nature Structural & Molecular Biology  28, no. 3 (March 2021): 290–299. PMID 33633399

  • Dong, X., Yang, Y., Zou, Z. et al. Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature  589, 456–461 (2021). PMID 33328639

 

 

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>Newsletter Archive

 

 

 

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>Facility News Archive

January 1, 2020

Dr. Daniela Nicastro has stepped down as Director of the CryoEM Facility at UTSW. If you are interested in cryoEM and/or the Facility, please contact the following people:

1) for general advice about using cryoEM in your research as non-expert-lab at UTSW, please contact Dr. Diana Tomchick (director of the single particle cryoEM service-for-fee program at UTSW).

2) for inquiries about Facility operations, policies and hands-on training, please contact the Facility manager Dr. Daniel Stoddard, or the (interims) Facility directors Drs. Michael Rosen and Sandra Schmid.

September 1, 2018

The CEMF received a CPRIT Core Facility Support Award - $5,5 Mill.

The award will support: 1) Operations of the Cryo-Electron Microscopy Core Facility at UTSW by contributing to staff salaries and instrument service contracts; 2) purchase of new equipment to increase efficiency of cryo-sample-preparation and sample screening; and 3) it will support a Service Facility for Single-Particle Cryo-EM structure determination, which will be especially beneficial for all those UTSW labs that would like to benefit from this state-of-the-art technique and facility, but don’t plan to become EM experts and/or invest several months into training of lab members, such as labs focused on cancer research.

December 11, 2017

The success continues: collaborative effort by the Bai and Jiang labs results in the second Nature publication this year.

TRPM4 is a calcium-activated, PI(4,5)P2-modulated, non-selective cation channel that plays important roles in many physiological processes such as insulin secretion in pancreatic β cells and breath pace-making in brainstem neurons, and its mutations was found to be associated with human heart conduction dysfunction. The labs from Dr. Xiao-chen Bai and Dr. Youxing Jiang determined the single particle cryo-EM structures of the mouse TRPM4 channel in the apo- and ATP-bound states with 3.1 Å and 2.9 Å resolution, respectively (Guo et al. Nature, 2017). Along with electrophysiological analysis, this study not only reveals the unique molecular architecture of the TRPM family, but also elucidates the structural basis of ATP modulation and ion selectivity of the TRPM4 channel.

subcellular structures in increasing resolution

October 7, 2017

First publication of an atomic protein structure determined using the CEMF

The collaborative effort of Dr. Youxing Jiang’s group (Physiology and Biophysics) and Dr. Xiao-chen Bai’s group (Biophysics and Cell biology) resulted in the world’s first 3D atomic structure of a mammalian ion channel Transient receptor potential mucolipin 1 (TRPML1) (Chen*, She* et al., Nature, 2017). TRPML1 is an endo/lysosomal cation channel, and its loss-of-function mutations are the direct cause of Type IV mucolipidosis (MLIV), an autosomal recessive lysosomal storage disease. By using single particle cryo-electron microscopy (cryo-EM) in combination with mutagenesis, the TRPML1 structure reveals the PIP2 binding site and several key features in the selectivity filter that determine the cation ion selectivity. Through a particles sorting approach, the structure also reveals two equally distributed S4-S5 linker conformations in the closed channel, providing structural implication for the S4-S5 linker-mediated PIP2 gating mechanism among TRPML channels. This work marks the first publication of a structure determined using the university’s new $17 million Cryo-Electron Microscopy Facility (CEMF).

subcellular structures in increasing resolution

October 7, 2017

Come join us to celebrate the EXCITING WIN for the field of Cryo-Electron Microscopy!!!

We will celebrate this Friday October 6th at 5:00 PM in the NL5 elevator lounge (3 elevator side). I hope you will find time to come by for a toast and snacks.

subcellular structures in increasing resolution

April 6, 2017

Single-Particle Discussion Group begins

First Thursday of each month, 4-5 p.m., NB10.606

To address the needs of the nascent cryo-EM single-particle reconstruction community at UT Southwestern, we have organized a monthly group to discuss methods and strategies to tackle problems as they arise. This will be of most use to people that have already collected some cryo-EM data; however all are welcome to attend. The format will consist of very informal conversations about specific problems. People who have questions can prepare two or three slides to provide a brief introduction of the project background and the nature of the problem. (Images may include raw micrographs, 2D averages, or a slice of a 3D reconstruction.)

As with all informal lab meetings/discussion groups on campus, the material presented is considered confidential.

March 31, 2017

Farewell Happy Hour for Kangkang Song

Dany’s lab will have a special Happy Hour to say farewell to Dr. Kangkang Song, who will start in April as EM facility manager at the University of Massachusetts. Please feel free to join us!

March 28, 2017

Volta Phase Plate (VPP) Data

Dany presents Volta Phase Plate (VPP) data at Cell Biology Faculty Works in Progress, showing contrast and resolution improvement compared to previous subtomogram averages: the “96nm ruler” (coiled-coil, arrow) is visible with just 200 particles averaged.

subcellular structures in increasing resolution

March 20, 2017

Polices and Training Implemented

The CEMF's Policies, Rules, and Rates have been approved by the Internal Advisory Committee; user training has begun on the Talos Arctica electron microscope.

November 2016

Arrival of Talos™ Arctica

Room under construction
Preparing the room for arrival
Faculty members posing with machine
Drs. Michael Rosen and Sandra Schmid pose with the newly delivered microscope.

June 2016

News Coverage of CEMF

Drs. Sandra Schmid, Michael Rosen and Daniela Nicastro are interviewed by WNDU16.

May 25, 2016

KERA Interview

Dr. Michael Rosen is interviewed by Justin Martin for KERA Breakthroughs.

May 16, 2016

CEMF News Release

“We are the only institution in the world with this configuration of instruments,” said Dr. Sandra Schmid, Chair of the Department of Cell Biology and holder of the Cecil H. Green Distinguished Chair in Cellular and Molecular Biology. “It establishes UT Southwestern as one of the world’s top facilities for cryo-EM structural biology.”
Read full release

Banner featuring Drs. Rosen, Schmid, and Nicastro
The news release is featured on UT Southwestern's home page.

April 25, 2016

Inaugural Symposium

Symposium flyer

A symposium will celebrate the CEMF's grand opening will of the CEMF. “The Resolution Revolution: New Windows into Cellular Structure and Function” will feature distinguished guest speakers from universities nationwide.

March 14, 2016

Panorama of Krios Room

Panorama image of empty room
Panorama shot of NL1.180D, waiting for the Krios to arrive

2015-2016

Construction of CEMF Annex

Building in various stages of construction
The annex housing the new CEMF is shown on August 24, 2015 (left), October 19, 2015 (center), and March 1, 2016 (right)

 

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>Publications acknowledging the CEMF

 

2021

  • Lu, D., Shang, G., He, X., Bai, X.-C., & Zhang, X. (2021). Architecture of the sema3a/plexina4/neuropilin tripartite complex. Nature Communications , 12(1), 3172. PMID 34039996

  • Uchikawa, E., Chen, Z., Xiao, G.-Y., Zhang, X., & Bai, X.-C. (2021). Structural basis of the activation of c-MET receptor. Nature Communications,  12(1), 4074. PMID 34210960

  • Kober, D. L., Radhakrishnan, A., Goldstein, J. L., Brown, M. S., Clark, L. D., Bai, X.-C., & Rosenbaum, D. M. (2021). Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing.  Cell , 184(14), 3689-3701.e22. PMID 34139175

  • Noviello, Colleen M., Anant Gharpure, Nuriya Mukhtasimova, Rico Cabuco, Leah Baxter, Dominika Borek, Steven M. Sine, and Ryan E. Hibbs. “Structure and Gating Mechanism of the Α7 Nicotinic Acetylcholine Receptor.”  Cell  184, no. 8 (April 15, 2021): 2121-2134.e13. PMID 33735609

  • Jeong, Byung-Cheon, Sung Jun Bae, Lisheng Ni, Xuewu Zhang, Xiao-Chen Bai, and Xuelian Luo. “Cryo-EM Structure of the Hippo Signaling Integrator Human STRIPAK.” Nature Structural & Molecular Biology  28, no. 3 (March 2021): 290–299. PMID 33633399

  • Dong, X., Yang, Y., Zou, Z. et al. Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature  589, 456–461 (2021). PMID 33328639

2020

  • Qi, Xiaofeng, Lucas Friedberg, Ryan De Bose-Boyd, Tao Long, and Xiaochun Li. “Sterols in an Intramolecular Channel of Smoothened Mediate Hedgehog Signaling.”Nature Chemical Biology 16, no. 12 (December 2020): 1368–1375. PMID 32929279

  • Kim JJ, Gharpure A, Teng J, et al. (2020) Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature 2020; 585(7824):303-308. PMID 32879488

  • Yin J, Chen KM, Clark MJ, et al. (2020) Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane. Nature 2020;584(7819):125-129. PMID 32528175

  • Li F, Li Y, Ye X, et al. (2020) Cryo-EM structure of VASH1-SVBP bound to microtubules. Elife 2020;9 PMID 32773040

  • Long T, Qi X, Hassan A, Liang Q, De brabander JK, Li X. (2020) Structural basis for itraconazole-mediated NPC1 inhibition. Nat Commun 2020;11(1):152. PMID 31919352

  • Kuo YC, Chen H, Shang G, et al. (2020) Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation. Nat Commun 2020;11(1):1953. PMID 32327662

  • Wang R, Long T, Hassan A, et al. (2020) Cryo-EM structures of intact V-ATPase from bovine brain. Nat Commun 2020;11(1):3921. PMID 32764564

  • Zhang X, Bai XC, Chen ZJ. (2020) Structures and Mechanisms in the cGAS-STING Innate Immunity Pathway. Immunity 2020;53(1):43-53. PMID 32668227

  • Shi Z, Gao H, Bai XC, Yu H. (2020) Cryo-EM structure of the human cohesin-NIPBL-DNA complex. Science 2020;368(6498):1454-1459. PMID 32409525

  • Peng W, Casey AK, Fernandez J, et al. (2020) A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM. Nat Struct Mol Biol 2020;27(6):589-597. PMID 32424347

  • Long T, Sun Y, Hassan A, Qi X, Li X. (2020) Structure of nevanimibe-bound tetrameric human ACAT1. Nature 2020;581(7808):339-343. PMDI 32433613

  • Partin AC, Zhang K, Jeong BC, et al. (2020) Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Mol Cell 2020;78(3):411-422.e4. PMID 32220646

  • Bromberg R, Guo Y, Borek D, Otwinowski Z. (2020) High-resolution cryo-EM reconstructions in the presence of substantial aberrations. IUCrJ. 2020;7(Pt 3):445-452. PMID 32431828

  • Qi X, Friedberg L, De bose-boyd R, Long T, Li X. (2020) Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling. Nat Chem Biol. 2020; PMID 32929279

  • Wang R, Qi X, Schmiege P, Coutavas E, Li X. (2020) Marked structural rearrangement of mannose 6-phosphate/IGF2 receptor at different pH environments. Sci Adv. 2020;6(7):eaaz1466. PMID 32095534

2019

  • Gui L, Song K, Tritschler D, et al. (2019) Scaffold subunits support associated subunit assembly in the ciliary nexin-dynein regulatory complex. Proc Natl Acad Sci USA 2019;116(46):23152-23162. PMID 31659045

  • Li J, Shang G, Chen YJ, et al. (2019) Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. Elife 2019;8 PMID 31535977

  • Uchikawa E, Choi E, Shang G, Yu H, Bai XC. (2019) Activation mechanism of the insulin receptor revealed by cryo-EM structure of the fully liganded receptor-ligand complex. Elife 2019;8 PMID 31436533

  • Prinslow EA, Stepien KP, Pan YZ, Xu J, Rizo J (2019) Multiple factors maintain assembled trans-SNARE complexes in the presence of NSF and αSNAP. eLife 8. pii: e38880. doi: 10.7554/eLife.38880.
  • Zhang C, Shang G, Gui X, Zhang X*, Bai X*, Chen ZJ* (2019) Structural basis of STING binding with and phosphorylation by TBK1. Nature 567:394-398. doi: 10.1038/s41586-019-1000-2

  • Shang G, Zhang C, Chen ZJ*, Bai X*, Zhang X* (2019) Cryo-EM structures of STING reveal its mechanism of activation by cyclic GMP-AMP. Nature 567:389-393. doi: 10.1038/s41586-019-0998-5

  • Quade B, Camacho M, Zhao X, Orlando M, Trimbuch T, Xu J, Li W, Nicastro D, Rosenmund C, Rizo J (2019) Membrane bridging by Munc13-1 is crucial for neurotransmitter release. eLife 8:e42806. [PMCID: PMC6407922]

  • She J, Zeng W, Guo J, Chen Q, Bai X*, Jiang Y* (2019) Structural mechanisms of phospholipid activation of the human TPC2 channel. eLife 8. pii: e45222. doi: 10.7554/eLife.45222

  • Hariri H, Speer N, Bowerman J, Rogers S, Fu G, Reetz E, Datta S, Feathers JR, Ugrankar R, Nicastro D, Henne WM (2019) Mdm1 maintains endoplasmic reticulum homeostasis by spatially regulating lipid droplet biogenesis. J Cell Biol. jcb.201808119. [PMCID: PMC6446837]

  • Spietz RL, Lundeen RA, Zhao X, Nicastro D, Ingalls AE, Morris RM (2019) Heterotrophy within a sulfur-oxidizing lineage of chemoautotrophic marine bacteria. Environ MicrobiolDOI: https://doi.org/10.1111/1462-2920.14623

  • Chen Q, Zeng W, She J, Bai XC, Jiang Y (2019) Structural and functional characterization of an otopetrin family proton channel. eLife8. pii: e46710. doi: 10.7554/eLife.46710

  • Shah V*, Zhao X*, Lundeen RA, Ingalls AE, Nicastro D, Morris RM (2019) Morphological plasticity in a sulfur-oxidizing bacterium from the SUP05 clade enhances dark carbon fixation. mBio DOI: 10.1128/mBio.00216-19. [PMCID: PMC6509183]

  • Wang Y, Nguyen NX, She J, Zeng W, Yang Y, Bai X*, Jiang Y* (2019) Structural mechanism of EMRE-dependent gating of the human mitochondrial calcium uniporter. Cell 177(5):1252-1261.e13. doi: 10.1016/j.cell.2019.03.050.

  • Qi X, Liu H, Thompson B, McDonald J, Zhang C, Li X (2019) Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric Gi. Nature 571:279-283. doi: 10.1038/s41586-019-1286-0.

  • Peng W, de Souza Santos M, Li Y, Tomchick DR, Orth K (2019) High-resolution cryo-EM structures of the E. coli hemolysin ClyA oligomers. PLoS One 14:e0213423. doi: 10.1371/journal.pone.0213423.

  • Qi X, Liu H, Thompson B, McDonald J, Zhang C, Li X (2019) Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric Gi. Nature 571:279-283. doi: 10.1038/s41586-019-1286-0.
  • Peng W, de Souza Santos M, Li Y, Tomchick DR, Orth K (2019) High-resolution cryo-EM structures of the E. coli hemolysin ClyA oligomers. PLoS One 14:e0213423. doi: 10.1371/journal.pone.0213423.
  • Dymek EE, Lin J*, Fu G*, Porter ME, Nicastro D, Smith EF (2019) PACRG and FAP20 form the inner junction of axonemal doublet microtubules and regulate ciliary motility. Mol Biol Cell 30:1805-1816. [PMCID: PMC6727744]
  • Gharpure A, Noviello C, Teng J, Zaveri N, Hibbs R (2019) Agonist selectivity and ion permeation in the α3β4 ganglionic nicotinic receptor. Neuron 104:501-511.e6. doi: 10.1016/j.neuron.2019.07.030.
  • Uchikawa E*, Choi E*, Shang G, Yu H#, Bai X# (2019) Activation mechanism of the insulin receptor revealed by cryo-EM structure of the fully liganded receptor-ligand complex. eLife 8. pii: e48630. doi: 10.7554/eLife.48630
  • Li J*, Shang G*, Chen YJ, Brautigam CA, Liou J, Zhang X#, Bai X# (2019) Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. eLife 8. pii: e47650. doi: 10.7554/eLife.47650
  • Lin J*, Le TV*, Augsperger K, Tritschler D, Bower R, Fu G, Perrone C, O’Toole ET, VanderWaal Mills K, Dymek EE, Smith EF, Nicastro D*, Porter ME* (2019) FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia. Mol Biol Cell 30:2659-2680, doi: 10.1091/mbc.E19-07-0367 [PMCID: PMC6761771]
  • Li J, Choi E, Yu H, Bai XC (2019) Structural basis of the activation of type 1 insulin-like growth factor receptor. Nat Commun 10:4567. doi: 10.1038/s41467-019-12564-0
  • Fu G*, Zhao L*, Dymek E, Hou Y, Song K, Phan N, Shang Z, Smith EF, Witman GB, Nicastro D (2019) Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus. J Cell Biol. pii: jcb.201906006. doi: 10.1083/jcb.201906006. [Epub ahead of print]
  • Gui L, Song K, Tristchler D, Bower R, Si Y, Dai A, Augsperger K, Sakizadeh J, Grzemska M, Ni T, Porter ME, Nicastro D (2019) Scaffold subunits support associated subunit assembly in the Chlamydomonas ciliary nexin-dynein regulatory complex. PNAS pii: 201910960. doi: 10.1073/pnas.1910960116. [Epub ahead of print]
  • Trötschel C, Hamzeh H, Alvarez L, Pascal R, Lavryk F, Bönigk W, Körschen HG, Müller A, Poetsch A, Rennhack A, Gui L, Nicastro D, Strünker T, Seifert R, Kaupp UB (2019) Absolute proteomic quantification reveals design principles of flagellar chemosensation. EMBO J(accepted)
  • Bromberg R, Guo Y, Borek D, Otwinowski Z (2019) High-resolution cryo-EM reconstructions in the presence of substantial aberrations. bioRxiv doi: https://doi.org/10.1101/798280 

 

2018

  • She J, Guo J, Chen Q, Zeng W, Jiang Y* & Bai X* (2018). Structural insights into the voltage and phospholipid activation of mammalian TPC1 channel. Nature 556, 130-134. doi:10.1038/nature26139.
  • Fu G, Wang Q, Phan N, Urbanska P, Joachimiak E, Wloga D, Nicastro D (2018) The I1 dynein-associated tether and tether head complex is a conserved regulator of ciliary motility. Mol Biol Cell 29:1048-1059. [PMCID: PMC5921572]
  • Nguyen NX, Armache JP, Lee C, Yang Y, Zeng W, Mootha VK, Cheng Y, Bai X* & Jiang Y* (2018). Cryo-EM structure of a fungal mitochondrial calcium uniporter. Nature 559, 570-574. doi: 10.1038/s41586-018-0333-6.
  • Walsh RM Jr, Roh SH, Gharpure A, Morales-Perez CL, Teng J, Hibbs RE (2018). Structural principles of distinct assemblies of the human α4β2 nicotinic receptor. Nature 557(7704):261-265. [PMCID PMC6132059]
  • Zhu S, Noviello CM, Teng J, Walsh RM Jr, Kim JJ, Hibbs RE (2018). Structure of a human synaptic GABAA receptor. Nature 559(7712):67-72.
  • Qi X, Schmiege P, Coutavas E, Wang J, Li X (2018). Structures of human Patched and its complex with native palmitoylated Sonic Hedgehog. Nature 560: 128–132.
  • Fine M, Schmiege P, Li X (2018). Structural basis for PtdInsP2mediated human TRPML1 regulation. Nature Comm 9:4192.
  • Qi X, Schmiege P, Coutavas E, Xiaochun Li (2018). Two Patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex. Science 362: 52. pii: eaas8843.

 

2017

  • Guo J, She J, Zeng W, Chen Q, Bai X* & Jiang Y* (2017). Structures of the Calcium-activated Non-Selective Cation Channel TRPM4. Nature 552, 205–209. doi:10.1038/nature24997.
  • Chen Q, She J, Zeng W, Guo J, Xu H, Bai X* & Jiang Y* (2017). Structure of mammalian endolysosomal TRPML1 channel in nanodiscs. Nature 550, 415-418. doi:10.1038/nature24035.