Publications using the UCSF CryoEM Core

2024

  • Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking. Chio US, Palovcak E, Smith AAA, Autzen H, Muñoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y. Nat Commun. 2024 Mar 12;15(1):2225. https://pubmed.ncbi.nlm.nih.gov/38472177/
  • Structural dynamics of the active HER4 and HER2/HER4 complexes is finely tuned by different growth factors and glycosylation. Trenker R, Diwanji D, Bingham T, Verba KA, Jura N. Elife. 2024 Mar 18:12:RP92873. https://pubmed.ncbi.nlm.nih.gov/38498590/
  • Structural basis of prostaglandin efflux by MRP4. Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM. Nat Struct Mol Biol. 2024 Apr;31(4):621-632. https://pubmed.ncbi.nlm.nih.gov/38216659/
  • GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter JF, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. Nat Struct Mol Biol. 2024 Apr;31(4):667-677. https://pubmed.ncbi.nlm.nih.gov/38326651/
  • Antibody discovery identifies regulatory mechanisms of protein arginine deiminase 4. Zhou X, Kong S, Maker A, Remesh SG, Leung KK, Verba KA, Wells JA. Nat Chem Biol. 2024 Jun;20(6):742-750. https://pubmed.ncbi.nlm.nih.gov/38308046/
  • Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome. Zhao B, Cao Z, Zheng Y, Nguyen P, Bowen A, Edwards RH, Stroud RM, Zhou Y, Van Lookeren Campagne M, Li F. Nat Commun. 2024 Jun 25;15(1):5388. https://pubmed.ncbi.nlm.nih.gov/38918376/
  • Poc1 bridges basal body inner junctions to promote triplet microtubule integrity and connections. Ruehle MD, Li S, Agard DA, Pearson CG. J Cell Biol. 2024 Aug 5;223(8):e202311104. https://pubmed.ncbi.nlm.nih.gov/38743010/
  • High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Czarnik C, Gulati S, Lander GC, Verba KA. J Struct Biol. 2024 Sep;216(3):108108. https://pubmed.ncbi.nlm.nih.gov/38944401/
  • Structural basis of TRPV1 modulation by endogenous bioactive lipids. Arnold WR, Mancino A, Moss FR 3rd, Frost A, Julius D, Cheng Y. Nat Struct Mol Biol. 2024 Sep;31(9):1377-1385. https://pubmed.ncbi.nlm.nih.gov/38698206/
  • A systematic search for RNA structural switches across the human transcriptome. Khoroshkin M, Asarnow D, Zhou S, Navickas A, Winters A, Goudreau J, Zhou SK, Yu J, Palka C, Fish L, Borah A, Yousefi K, Carpenter C, Ansel KM, Cheng Y, Gilbert LA, Goodarzi H. Nat Methods. 2024 Sep;21(9):1634-1645. https://pubmed.ncbi.nlm.nih.gov/39014073/
  • Structural basis of μ-opioid receptor targeting by a nanobody antagonist. Yu J, Kumar A, Zhang X, Martin C, Van Holsbeeck K, Raia P, Koehl A, Laeremans T, Steyaert J, Manglik A, Ballet S, Boland A, Stoeber M. Nat Commun. 2024 Oct 9;15(1):8687. https://pubmed.ncbi.nlm.nih.gov/39384768/
  • Dynamic allostery drives autocrine and paracrine TGF-β signaling. Jin M, Seed RI, Cai G, Shing T, Wang L, Ito S, Cormier A, Wankowicz SA, Jespersen JM, Baron JL, Carey ND, Campbell MG, Yu Z, Tang PK, Cossio P, Wen W, Lou J, Marks J, Nishimura SL, Cheng Y. Cell. 2024 Oct 31;187(22):6200-6219.e23. https://pubmed.ncbi.nlm.nih.gov/39288764/
  • Engineered odorant receptors illuminate the basis of odour discrimination. de March CA, Ma N, Billesbølle CB, Tewari J, Llinas Del Torrent C, van der Velden WJC, Ojiro I, Takayama I, Faust B, Li L, Vaidehi N, Manglik A, Matsunami H. Nature. 2024 Oct 30. https://pubmed.ncbi.nlm.nih.gov/39478229/
2023
  • The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nieweglowska ES, Brilot AF, Méndez-Moran M, Kokontis C, Baek M, Li J, Cheng Y, Baker D, Bondy-Denomy J, Agard DA. Nat Commun. 2023 Feb 18;14(1):927. https://pubmed.ncbi.nlm.nih.gov/36807264/
  • Brominated lipid probes expose structural asymmetries in constricted membranes. Moss FR 3rd, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A. Nat Struct Mol Biol. 2023 Feb;30(2):167-175. https://pubmed.ncbi.nlm.nih.gov/36624348/
  • The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD. Nature. 2023 Mar;615(7953):728-733. https://pubmed.ncbi.nlm.nih.gov/36754086/
  • Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. Nat Struct Mol Biol. 2023 Mar;30(3):296-308. https://pubmed.ncbi.nlm.nih.gov/36782050/
  • Structural basis of odorant recognition by a human odorant receptor. Billesbølle CB, de March CA, van der Velden WJC, Ma N, Tewari J, Del Torrent CL, Li L, Faust B, Vaidehi N, Matsunami H, Manglik A. Nature. 2023 Mar;615(7953):742-749. https://pubmed.ncbi.nlm.nih.gov/36922591/
  • In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes. Chen Z, Greenan GA, Shiozaki M, Liu Y, Skinner WM, Zhao X, Zhao S, Yan R, Yu Z, Lishko PV, Agard DA, Vale RD. Nat Struct Mol Biol. 2023 Mar;30(3):360-369. https://pubmed.ncbi.nlm.nih.gov/36593309/
  • The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD. Nature. 2023 Mar;615(7953):728-733. https://pubmed.ncbi.nlm.nih.gov/36754086/
  • Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH Jr, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Mehmood H, Pawar KI, Pourmal S, Smith AM, Zhou F; QCRG Structural Biology Consortium; DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA. Structure. 2023 Mar 2;31(3):253-264.e6. https://pubmed.ncbi.nlm.nih.gov/36805129/
  • Hsp90 provides a platform for kinase dephosphorylation by PP5. Jaime-Garza M, Nowotny CA, Coutandin D, Wang F, Tabios M, Agard DA. Nat Commun. 2023 Apr 17;14(1):2197. https://pubmed.ncbi.nlm.nih.gov/37069154/
  • Dodecamer assembly of a metazoan AAA+ chaperone couples substrate extraction to refolding. Gupta A, Lentzsch AM, Siegel A, Yu Z, Chio US, Cheng Y, Shan SO. Sci Adv. 2023 May 10;9(19):eadf5336. https://pubmed.ncbi.nlm.nih.gov/37163603/
  • Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Singh I, Seth A, Billesbølle CB, Braz J, Rodriguiz RM, Roy K, Bekele B, Craik V, Huang XP, Boytsov D, Pogorelov VM, Lak P, O'Donnell H, Sandtner W, Irwin JJ, Roth BL, Basbaum AI, Wetsel WC, Manglik A, Shoichet BK, Rudnick G. Cell. 2023 May 11;186(10):2160-2175.e17. https://pubmed.ncbi.nlm.nih.gov/37137306/
  • Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawłowski K, Krogan NJ, Jura N, Verba KA. Nat Commun. 2023 Jun 19;14(1):3543. https://pubmed.ncbi.nlm.nih.gov/37336883/
  • Structural basis for CaVα2δ:gabapentin binding. Chen Z, Mondal A, Minor DL Jr. Nat Struct Mol Biol. 2023 Jun;30(6):735-739. https://pubmed.ncbi.nlm.nih.gov/36973510/
  • EMC chaperone-CaV structure reveals an ion channel assembly intermediate. Chen Z, Mondal A, Abderemane-Ali F, Jang S, Niranjan S, Montaño JL, Zaro BW, Minor DL Jr. Nature. 2023 Jul;619(7969):410-419. https://pubmed.ncbi.nlm.nih.gov/37196677/
  • Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Wu H, Muñoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y. Science. 2023 Jul 21;381(6655):319-324. https://pubmed.ncbi.nlm.nih.gov/37384669/
  • Structural mechanism of mitochondrial membrane remodelling by human OPA1. on der Malsburg A, Sapp GM, Zuccaro KE, von Appen A, Moss FR 3rd, Kalia R, Bennett JA, Abriata LA, Dal Peraro M, van der Laan M, Frost A, Aydin H. Nature. 2023 Aug;620(7976):1101-1108. https://pubmed.ncbi.nlm.nih.gov/37612504/
  • Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase. Feng S, Puchades C, Ko J, Wu H, Chen Y, Figueroa EE, Gu S, Han TW, Ho B, Cheng T, Li J, Shoichet B, Jan YN, Cheng Y, Jan LY. Nat Commun. 2023 Aug 12;14(1):4874. https://pubmed.ncbi.nlm.nih.gov/37573365/
  • Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Proc Natl Acad Sci. 2023 Aug;120(31):e2302471120. https://pubmed.ncbi.nlm.nih.gov/37487103/
  • De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking. Chen Z, Shiozaki M, Haas KM, Skinner WM, Zhao S, Guo C, Polacco BJ, Yu Z, Krogan NJ, Lishko PV, Kaake RM, Vale RD, Agard DA. Cell. 2023 Nov 9;186(23):5041-5053.e19. https://pubmed.ncbi.nlm.nih.gov/37865089/
  • A helical fulcrum in eIF2B coordinates allosteric regulation of stress signaling. Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S. Nat Chem Biol. 2024 Apr;20(4):422-431. https://pubmed.ncbi.nlm.nih.gov/37945896/
  • Assembly of SARS-CoV-2 ribonucleosomes by truncated N∗ variant of the nucleocapsid protein. Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. J Biol Chem. 2023 Dec;299(12):105362. https://pubmed.ncbi.nlm.nih.gov/37863261/
  • Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor. Noddings CM, Johnson JL, Agard DA. Nat Struct Mol Biol. 2023 Dec;30(12):1867-1877. https://pubmed.ncbi.nlm.nih.gov/37945740/