Yifan Cheng, PhD

Associate Professor
Biochemistry and BIophysics
[email protected]
+1 415 514-9708

We are interested in studying the three-dimensional structures of macromolecular complexes: their structural architectures, the regulation of their function and the dynamic processes of their assembly and disassembly, by molecular electron microscopy (cryoEM). A full understanding of the biological functions/processes of any macromolecular complex requires structural information at a wide range of resolutions, including atomic details of its components, spatial arrangements of these components and interactions between them. CryoEM can be used to study macromolecules in their native conformations at a wide resolution range, from sub-nanometer resolution (single particle cryoEM) to the cellular level (electron tomography).

Publications: 

Allosteric communication in the dynein motor domain.

Cell

Bhabha G, Cheng HC, Zhang N, Moeller A, Liao M, Speir JA, Cheng Y, Vale RD

Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter.

Nature

Kim J, Wu S, Tomasiak TM, Mergel C, Winter MB, Stiller SB, Robles-Colmanares Y, Stroud RM, Tampé R, Craik CS, Cheng Y

Selective targeting of TGF-ß activation to treat fibroinflammatory airway disease.

Science translational medicine

Minagawa S, Lou J, Seed RI, Cormier A, Wu S, Cheng Y, Murray L, Tsui P, Connor J, Herbst R, Govaerts C, Barker T, Cambier S, Yanagisawa H, Goodsell A, Hashimoto M, Brand OJ, Cheng R, Ma R, McKnelly KJ, Wen W, Hill A, Jablons D, Wolters P, Kitamura H, Araya J, Barczak AJ, Erle DJ, Reichardt LF, Marks JD, Baron JL, Nishimura SL

Single particle electron cryo-microscopy of a mammalian ion channel.

Current opinion in structural biology

Liao M, Cao E, Julius D, Cheng Y

Structural mechanism of serum amyloid A-mediated inflammatory amyloidosis.

Proceedings of the National Academy of Sciences of the United States of America

Lu J, Yu Y, Zhu I, Cheng Y, Sun PD

CTER-rapid estimation of CTF parameters with error assessment.

Ultramicroscopy

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

Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway.

Developmental cell

Asensio CS, Sirkis DW, Maas JW, Egami K, To TL, Brodsky FM, Shu X, Cheng Y, Edwards RH

Influence of electron dose rate on electron counting images recorded with the K2 camera.

Journal of structural biology

Li X, Zheng SQ, Egami K, Agard DA, Cheng Y

Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis.

Cell

Qian MX, Pang Y, Liu CH, Haratake K, Du BY, Ji DY, Wang GF, Zhu QQ, Song W, Yu Y, Zhang XX, Huang HT, Miao S, Chen LB, Zhang ZH, Liang YN, Liu S, Cha H, Yang D, Zhai Y, Komatsu T, Tsuruta F, Li H, Cao C, Li W, Li GH, Cheng Y, Chiba T, Wang L, Goldberg AL, Shen Y, Qiu XB

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.

Nature methods

Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y

Reconfiguration of the proteasome during chaperone-mediated assembly.

Nature

Park S, Li X, Kim HM, Singh CR, Tian G, Hoyt MA, Lovell S, Battaile KP, Zolkiewski M, Coffino P, Roelofs J, Cheng Y, Finley D

A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly.

Nature

Canzio D, Liao M, Naber N, Pate E, Larson A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R, Schuck P, Cheng Y, Narlikar GJ

Recording high-resolution images of two-dimensional crystals of membrane proteins.

Methods in molecular biology (Clifton, N.J.)

Avila-Sakar A, Li X, Zheng SQ, Cheng Y

A method for integrative structure determination of protein-protein complexes.

Bioinformatics (Oxford, England)

Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A

Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils.

Biomacromolecules

Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S

Fabs enable single particle cryoEM studies of small proteins.

Structure (London, England : 1993)

Wu S, Avila-Sakar A, Kim J, Booth DS, Greenberg CH, Rossi A, Liao M, Li X, Alian A, Griner SL, Juge N, Yu Y, Mergel CM, Chaparro-Riggers J, Strop P, Tampé R, Edwards RH, Stroud RM, Craik CS, Cheng Y

Self-assembly of amelogenin proteins at the water-oil interface.

European journal of oral sciences

Martinez-Avila OM, Wu S, Cheng Y, Lee R, Khan F, Habelitz S

Direct membrane association drives mitochondrial fission by the Parkinson disease-associated protein alpha-synuclein.

The Journal of biological chemistry

Nakamura K, Nemani VM, Azarbal F, Skibinski G, Levy JM, Egami K, Munishkina L, Zhang J, Gardner B, Wakabayashi J, Sesaki H, Cheng Y, Finkbeiner S, Nussbaum RL, Masliah E, Edwards RH

A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.

Ultramicroscopy

Zheng SQ, Branlund E, Kesthelyi B, Braunfeld MB, Cheng Y, Sedat JW, Agard DA

Self-aligning amelogenin nanoribbons in oil-water system.

Journal of structural biology

He X, Wu S, Martinez-Avila O, Cheng Y, Habelitz S

Structure characterization of the 26S proteasome.

Biochimica et biophysica acta

Kim HM, Yu Y, Cheng Y

HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.

Proceedings of the National Academy of Sciences of the United States of America

Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD

Collecting electron crystallographic data of two-dimensional protein crystals.

Methods in enzymology

Hite RK, Schenk AD, Li Z, Cheng Y, Walz T

HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells.

Traffic (Copenhagen, Denmark)

Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, Peterlin BM

The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes.

Nature

Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A, Purcell TJ, Cooke R, Cheng Y, Narlikar GJ

Toward an atomic model of the 26S proteasome.

Current opinion in structural biology

Cheng Y

Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases.

Molecular cell

Rabl J, Smith DM, Yu Y, Chang SC, Goldberg AL, Cheng Y

A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies.

Proceedings of the National Academy of Sciences of the United States of America

Frey G, Peng H, Rits-Volloch S, Morelli M, Cheng Y, Chen B

In vitro self-assembly of tailorable nanotubes from a simple protein building block.

Proceedings of the National Academy of Sciences of the United States of America

Ballister ER, Lai AH, Zuckermann RN, Cheng Y, Mougous JD

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

Molecular cell

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

Polymorphic assemblies and crystalline arrays of lens tetraspanin MP20.

Journal of molecular biology

Gonen T, Hite RK, Cheng Y, Petre BM, Kistler J, Walz T

Reconstructing the endocytotic machinery.

Methods in cell biology

Cheng Y, Walz T

Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.

Journal of molecular biology

Cheng Y, Boll W, Kirchhausen T, Harrison SC, Walz T

Activation of leukocyte beta2 integrins by conversion from bent to extended conformations.

Immunity

Nishida N, Xie C, Shimaoka M, Cheng Y, Walz T, Springer TA

Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled S2 domain.

Journal of molecular biology

Liu J, Wu S, Reedy MC, Winkler H, Lucaveche C, Cheng Y, Reedy MK, Taylor KA

Structure determination of clathrin coats to subnanometer resolution by single particle cryo-electron microscopy.

Journal of structural biology

Fotin A, Kirchhausen T, Grigorieff N, Harrison SC, Walz T, Cheng Y

Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.

Nature

Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T

Single particle reconstruction of the human apo-transferrin-transferrin receptor complex.

Journal of structural biology

Cheng Y, Zak O, Aisen P, Harrison SC, Walz T

Single particle reconstructions of the transferrin-transferrin receptor complex obtained with different specimen preparation techniques.

Journal of molecular biology

Cheng Y, Wolf E, Larvie M, Zak O, Aisen P, Grigorieff N, Harrison SC, Walz T

Molecular model for a complete clathrin lattice from electron cryomicroscopy.

Nature

Fotin A, Cheng Y, Sliz P, Grigorieff N, Harrison SC, Kirchhausen T, Walz T

Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating.

Nature

Fotin A, Cheng Y, Grigorieff N, Walz T, Harrison SC, Kirchhausen T

Aquaporin-0 membrane junctions form upon proteolytic cleavage.

Journal of molecular biology

Gonen T, Cheng Y, Kistler J, Walz T

Aquaporin-0 membrane junctions reveal the structure of a closed water pore.

Nature

Gonen T, Sliz P, Kistler J, Cheng Y, Walz T

A chimeric protein of simian immunodeficiency virus envelope glycoprotein gp140 and Escherichia coli aspartate transcarbamoylase.

Journal of virology

Chen B, Cheng Y, Calder L, Harrison SC, Reinherz EL, Skehel JJ, Wiley DC

Structure of the human transferrin receptor-transferrin complex.

Cell

Cheng Y, Zak O, Aisen P, Harrison SC, Walz T

The crystal structure of the bifunctional primase-helicase of bacteriophage T7.

Molecular cell

Toth EA, Li Y, Sawaya MR, Cheng Y, Ellenberger T

Structure of the Sec23p/24p and Sec13p/31p complexes of COPII.

Proceedings of the National Academy of Sciences of the United States of America

Lederkremer GZ, Cheng Y, Petre BM, Vogan E, Springer S, Schekman R, Walz T, Kirchhausen T

The three-dimensional map of microsomal glutathione transferase 1 at 6 A resolution.

The EMBO journal

Schmidt-Krey I, Mitsuoka K, Hirai T, Murata K, Cheng Y, Fujiyoshi Y, Morgenstern R, Hebert H

The projection structure of the membrane protein microsomal glutathione transferase at 3 A resolution as determined from two-dimensional hexagonal crystals.

Journal of molecular biology

Schmidt-Krey I, Murata K, Hirai T, Mitsuoka K, Cheng Y, Morgenstern R, Fujiyoshi Y, Hebert H

Influence of various nucleotides on the in situ crystallization of Ca2+-ATPase.

Biochimica et biophysica acta

Hiroaki Y, Mitsuoka K, Cheng Y, Hiroaki H, Fujiyoshi Y

The use of electron tomography for structural analysis of disordered protein arrays.

Journal of structural biology

Taylor KA, Tang J, Cheng Y, Winkler H