The David Van Andel Advanced Cryo-Electron Microscopy Suite

Publications containing work performed by VARI’s Cryo-EM Suite are asked to follow these guidelines in their acknowledgements:

  • Acknowledge contributions by The David Van Andel Advanced Cryo-Electron Microscopy Suite by name in the manuscript.
  • Consider authorship for more significant intellectual and planning contributions.
  • Notify Suite staff of successful publications and awarded grant applications. This assists in tracking and maintaining institutional records, which help inform the Suite’s quality services.


Li H*, Burgie S*, Gannam ZTK, Li H#, Vierstra R.D#. (2022). Plant phytochromes are asymmetric dimers with unique signaling potential. Nature.
* Co-first authors
# Co-corresponding authors

Zang F, Georgescu RE, Yao NY, O’Donnell ME*, Li H*. (2022). DNA is loaded through the 911 DNA checkpoint clamp in the opposite direction of the PCNA clampNat Struc Mol Biol.
Co-corresponding authors

Dykstra H, Fisk C, LaRose C, Waldhart A, Meng X, Zhao G, Wu N. 2021. Mouse long-chain acyl-CoA synthetase 1 is active as a monomer. Arch Biochem Biophys 700:108773.

Du M, Yuan Z, Werneburg GT, Henderson NS, Chauhan H, Kovach A, Zhao G, Johl J, Li H, Thanassi DG. 2021. Processive dynamics of the usher assembly platform during uropathogenic Escherichia coli P pilus biogenesis. Nat Commun 12(1):5207.

Yu H, Haja DK, Schut GJ, Wu CH, Meng X, Zhao G, Li H, Adams MWW. 2020. Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life. Nat Commun 11(1):5953.

Xing C, Zhuang Y, Xu TH, Feng Z, Zhou XE, Chen M, Wang L, Meng X, Xue Y, Wang J, Liu H, McGuire TF, Zhao G, Melcher K, Zhang C, Xu HE, Xie XQ. 2020. Cryo-EM structure of the human cannabinoid receptor CB2-Gi signaling complex. Cell 180(4):645–654.e13.

Zhuang Y, Liu H, Zhou EX, Kumar Verma R, de Waal PW, Jang W, Xu TH, Wang L, Meng X, Zhao G, Kang Y, Melcher K, Fan H, Lambert NA, Xu E, Zhang. 2020. Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling. Nat Commun 11(1):885.

Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE, Melcher K, Jones PA. 2020. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature 586(7827):151–155.

Bai L, Kovach A, You Q, Hsu HC, Zhao G, Li H. 2019. Autoinhibition and activation mechanisms of the eukaryotic lipid flippase Drs2p-Cdc50p. Nat Commun 10:4142.

Kim JY, Yeom J, Zhao G, Calcaterra H, Munn J, Zhang P, Kotov N. 2019. Assembly of gold nanoparticles into chiral superstructures driven by circularly polarized light. J Am Chem Soc 141(30):11739–11744.

Yu H, Lupoli TJ, Kovach A, Meng X, Zhao G, Nathan CF, Li H. 2018. ATP hydrolysis-coupled peptide translocation mechanism of Mycobacterium tuberculosis ClpB. Proc Natl Acad Sci U S A 115(41):E9560–E9569.

Hu K, Jastrab JB, Zhang S, Kovach A, Zhao G, Darwin KH, Li H. 2018. Proteasome substrate capture and gate opening by the accessory factor PafE from Mycobacterium tuberculosis. J Biol Chem 293(13):4713–4723.

Du M, Yaun Z, Yu H, Henderson N, Sarowar S, Zhao G, Werneburg GT, Thanassi DG, Li H. 2018. Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD. Nature.

Kang Y*, Kuybeda O*, de Waal PW*, Mukherjee S, Van Eps N, Dutka P, Zhou XE, Bartesaghi A, Erramilli S, Morizumi T, Gu X, Yin Y, Liu P, Jiang Y, Meng X, Zhao G, Melcher K, Ernst OP, Kossiakoff AA, Subramaniam S, Xu HE. 2018. Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Nature.

Fan C*, Choi W*, Sun W, Du J#, Lü W#. 2018. Structure of the human lipid-gated cation channel TRPC3. eLife:e36852.

Yu H, Wu CH, Schut GJ, Haja DK, Zhao G, Peters JW, Adams MWW*, Li H*. 2018. Structure of an ancient respiratory systemCell.
*Co-corresponding authors

Bai L, Wang T, Zhao G, Kovach A, Li H. 2018. The atomic structure of a eukaryotic oligosaccharyltransferase complex. Nature.

Noguchi Y, Yuan Z, Bai L, Schneider S, Zhao G, Stillman B, Speck C, Li H. 2017. Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model. Proc Natl Acad Sci U S A.

Yang M, Chan H, Zhao G, Bahng JH, Zhang P, Kral P, Kotov NA. 2016. Self-assembly of nanoparticles into biomimetic capsid-like nanoshells. Nat Chem doi:10.1038/nchem.2641

Liu C, Perilla JP, Ning J, Lu M, Hou G, Ramalho R, Himes BA, Zhao G, Bedwell GJ, Byeon IJ, Ann J, Gronenborn AM, Prevelige PE, Rousso I, Aiken C, Polenova T, Schulten K, Zhang P. 2016. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Nat Commun 7:10714.

Zhao G*, Perilla JR*, Yufenyuy EL*, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. 2013. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497:643.
*Featured on Nature cover. This paper was selected as NIGMS Director’s Featured Research Advance in June 2013.

Yeom J, Yeom B, Chan H, Smith KW, Dominguez-Medina S, Bahng JH, Zhao G, Chang W, Chang SJ, Chuvilin A, Melnikau D, Rogach AL, Zhang P, Link S, Král P, Kotov NA 2015. Chiral templating of self-assembling nanostructures by circularly polarized light. Nat Mater 14:66–72.

Meng X*, Zhao G*, Yufenyuy E*, Ke D, Ning J, DeLucia M, Ahn J, Gronenborn AM, Aiken C, Zhang P. 2012. Protease cleavage leads to formation of mature trimer interface in HIV-1 capsid. PLoS Pathog 8(8): e1002886.
*Co-first author

Zhao G, Ke D, Vu T, Ahn J, Shah VB, Yang R, Aiken C, Charlton L, Gronenborn AM, Zhang P. 2011. Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces. PLoS Pathog 7(3): e1002009.

Byeon IJL, Meng X, Jung J, Zhao G, Yang R, Shi J, Ahn J, Concel J, Aiken C, Zhang P, Gronenborn AM. 2009. Structural convergence between Cryo-EM and NMR reveals novel intersubunit interactions critical for HIV-1 capsid assembly and function. Cell 139:780.


Ruan Z*, Haley E*, Orozco I*, Sabat M, Myers R, Roth R, Du J#, Lü W#. 2021. Structures of the TRPM5 channel elucidate mechanisms of activation and inhibition. Nat Struct Mol Biol.

Ruan Z*, Osei-Owusu J*, Du J, Qiu Z#, Lü W#. 2020. Structures and pH-sensing mechanism of the proton-activated chloride channel. Nature.

Huang Y, Winkler PA, Sun W, Lü W#, Du J#. 2018. Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium. Nature.
#Co-last authors

Ning J, Erdemci-Tandogan G, Yufenyuy EL, Wagner J, Himes BA, Zhao G, Aiken C, Zandi R, Zhang P. 2016. In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway. Nat Commun 7:13689.

Merg AD, Boatz JC, Mandal A, Zhao G, Mokashi-Punekar S, Liu C, Wang X, Zhang P, van der Wel PCA, Rosi NL. 2016. Peptide-directed assembly of single-helical gold nanoparticle superstructures exhibiting intense chiroptical activity. J Am Chem Soc 138(41):13655.

Cassidy C, Himes BA, Alvarez FJ, Ma J, Zhao G, Perilla JR, Schulten K, Zhang P. 2015. CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. eLife 10.7554/eLife.08419.

Rezikyan A, Jibben ZJ, Rock BA, Zhao G, Koeck FA, Nemanich RF, Treacy MM. 2015. Speckle suppression by decoherence in fuctuation electron microscopy. Microsc Microanal 21(6)1455–1474.

Park J, Nguyen TD, Silveira GQ, Bahng JH, Srivastava S, Zhao G, Sun K, Zhang P, Sharon C, Glotzer SC, Kotov NA. 2014. Terminal supraparticle assemblies from similarly charged protein molecules and nanoparticles. Nat Commun 5:3593.

Song C, Blaber MG, Zhao G, Zhang P, Fry HC, Schatz GC, Rosi NL. 2013. Tailorable plasmonic circular dichroism properties of helical nanoparticle superstructures. Nano Lett 13(7)3256–3261.

Jun S, Zhao G, Ning J, Zhang P. 2013. Correlative microscopy for 3D structural analysis of dynamic interactions. J Vis Exp (76):e50386.

Yang H, Ji X, Zhao G, Ning J, Zhao Q, Aiken C, Gronenborn AM, Zhang P, Xiong Y. 2012. Structural insight into HIV-1 capsid recognition by rhesus TRIM5α. Proc Natl Acad Sci U S A 109(45):18372–18377.

Wang K, Strunk K, Zhao G, Gray JL, Zhang P. 2012. 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. J Struct Biol 180(2):318–326.

Jun S, Ke D, Debiec K, Zhao G, Meng X, Ambrose Z, Gibson G, Watkins S, Zhang P. 2011. Direct visualization of HIV-1 infection using correlative live-cell microscopy and cryo-EM tomography. Structure 19(11):1573–1581.

Meng X, Zhao G, Zhang P. 2011. Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction. JoVE 54:3041.

Hwang L, Zhao G, Zhang P, Rosi N. 2011. Size-controlled peptide-directed synthesis of hollow spherical gold nanoparticle superstructures. Small 7: doi: 10.1002/smll.201100477.

Song C, Zhao G, Zhang P, Rosi N. 2010. Expeditious synthesis and assembly of sub-100 nm hollow spherical gold nanoparticle superstructures. J Am Chem Soc 132(40):14033–14035.

Zhao G, Treacy MMJ, Buseck PR. 2010. Fluctuation electron microscopy of medium range order in ion-irradiated zircon. Philosoph Mag 90, 4661–4677.

Zhao G, Rougée A, Treacy MMJ, Buseck PR. 2009. Medium-range order in molecular materials: Fluctuation electron microscopy for detecting fullerenes in disordered carbons. Ultramicroscopy 109(2):177–188.

Treacy MMJ, Kumar D, Rougée A, Zhao G, Buseck PR, McNulty I, Fan L, Rau C, Gibson JM. 2008. Glimpsing order within the disarray. J Phys Conf Ser 126(1).

Treacy MMJ, Kumar D, Rougée A, Zhao G, Buseck PR, McNulty I, Fan L, Rau C, Gibson JM. 2007. Probing medium-range structural correlations by fluctuation microscopy. J Phys Condens Matter 19(45).

Zhao G, Zhang Q, Zhang H, Yang G, Tang J, Zhou O, Qin LC. 2006. Field emission of single Cs doped carbon nanotube. Appl Phys Lett 89(26).

Zhao G, Zhang J, Zhang Q, Zhang H, Tang J, Zhou O, Qin LC. 2006. Fabrication and characterization of single nanotube emitters as point electron sources. Appl Phys Lett 89 (19).

Zhang H, Tang J, Zhang Q, Zhao G, Yang G, Zhang J, Zhou O, Qin LC. 2005. Field emission of electron from single LaB6 nanowires. Adv Mater 18, 87.

Zhang H, Zhang Q, Zhao G, Tang J, Zhou O, Qin LC. 2005. Single-crystalline GdB6 nanowire field emitters. J Am Chem Soc 127(38):13120–13121.