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Volumn 115, Issue 13, 2018, Pages 3362-3367

Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system

Author keywords

Cryo electron microscopy; DARPin; Protein cage; Protein design; Protein scaffold

Indexed keywords

DESIGNED ANKYRIN REPEAT PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG; PROTEIN;

EID: 85044414451     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1718825115     Document Type: Article
Times cited : (70)

References (44)
  • 1
    • 84955581565 scopus 로고    scopus 로고
    • The development of cryo-EM into a mainstream structural biology technique
    • Nogales E (2016) The development of cryo-EM into a mainstream structural biology technique. Nat Methods 13:24–27.
    • (2016) Nat Methods , vol.13 , pp. 24-27
    • Nogales, E.1
  • 2
    • 84955582151 scopus 로고    scopus 로고
    • How good can cryo-EM become?
    • Glaeser RM (2016) How good can cryo-EM become? Nat Methods 13:28–32.
    • (2016) Nat Methods , vol.13 , pp. 28-32
    • Glaeser, R.M.1
  • 3
    • 84969983828 scopus 로고    scopus 로고
    • Breaking cryo-EM resolution barriers to facilitate drug discovery
    • Merk A, et al. (2016) Breaking cryo-EM resolution barriers to facilitate drug discovery. Cell 165:1698–1707.
    • (2016) Cell , vol.165 , pp. 1698-1707
    • Merk, A.1
  • 4
    • 84924617498 scopus 로고    scopus 로고
    • 2.8-Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy
    • Campbell MG, Veesler D, Cheng A, Potter CS, Carragher B (2015) 2.8-Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife 4:e06380.
    • (2015) eLife , vol.4 , pp. e06380
    • Campbell, M.G.1    Veesler, D.2    Cheng, A.3    Potter, C.S.4    Carragher, B.5
  • 5
    • 84969627248 scopus 로고    scopus 로고
    • TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action
    • Gao Y, Cao E, Julius D, Cheng Y (2016) TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature 534:347–351.
    • (2016) Nature , vol.534 , pp. 347-351
    • Gao, Y.1    Cao, E.2    Julius, D.3    Cheng, Y.4
  • 6
    • 84958883175 scopus 로고    scopus 로고
    • 2.3-Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition
    • Banerjee S, et al. (2016) 2.3-Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 351:871–875.
    • (2016) Science , vol.351 , pp. 871-875
    • Banerjee, S.1
  • 7
    • 85019070009 scopus 로고    scopus 로고
    • An atomic structure of the human spliceosome
    • e14
    • Zhang X, et al. (2017) An atomic structure of the human spliceosome. Cell 169: 918–929.e14.
    • (2017) Cell , vol.169 , pp. 918-929
    • Zhang, X.1
  • 8
    • 85029782310 scopus 로고    scopus 로고
    • The cryo-electron microscopy structure of human transcription factor IIH
    • Greber BJ, et al. (2017) The cryo-electron microscopy structure of human transcription factor IIH. Nature 549:414–417.
    • (2017) Nature , vol.549 , pp. 414-417
    • Greber, B.J.1
  • 9
    • 85032875994 scopus 로고    scopus 로고
    • Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3
    • Hirschi M, et al. (2017) Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3. Nature 550:411–414.
    • (2017) Nature , vol.550 , pp. 411-414
    • Hirschi, M.1
  • 10
    • 0035956861 scopus 로고    scopus 로고
    • Nanohedra: Using symmetry to design self-assembling protein cages, layers, crystals, and filaments
    • Padilla JE, Colovos C, Yeates TO (2001) Nanohedra: Using symmetry to design self-assembling protein cages, layers, crystals, and filaments. Proc Natl Acad Sci USA 98: 2217–2221.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 2217-2221
    • Padilla, J.E.1    Colovos, C.2    Yeates, T.O.3
  • 11
    • 84861652462 scopus 로고    scopus 로고
    • Structure of a 16-nm cage designed by using protein oligomers
    • Lai Y-T, Cascio D, Yeates TO (2012) Structure of a 16-nm cage designed by using protein oligomers. Science 336:1129.
    • (2012) Science , vol.336 , pp. 1129
    • Lai, Y.-T.1    Cascio, D.2    Yeates, T.O.3
  • 12
    • 84877588832 scopus 로고    scopus 로고
    • Self-assembling cages from coiled-coil peptide modules
    • Fletcher JM, et al. (2013) Self-assembling cages from coiled-coil peptide modules. Science 340:595–599.
    • (2013) Science , vol.340 , pp. 595-599
    • Fletcher, J.M.1
  • 13
    • 84874061841 scopus 로고    scopus 로고
    • Re-engineering protein interfaces yields copper-inducible ferritin cage assembly
    • Huard DJE, Kane KM, Tezcan FA (2013) Re-engineering protein interfaces yields copper-inducible ferritin cage assembly. Nat Chem Biol 9:169–176.
    • (2013) Nat Chem Biol , vol.9 , pp. 169-176
    • Huard, D.J.E.1    Kane, K.M.2    Tezcan, F.A.3
  • 14
    • 84902006780 scopus 로고    scopus 로고
    • Accurate design of co-assembling multi-component protein nanomaterials
    • King NP, et al. (2014) Accurate design of co-assembling multi-component protein nanomaterials. Nature 510:103–108.
    • (2014) Nature , vol.510 , pp. 103-108
    • King, N.P.1
  • 15
    • 84979578745 scopus 로고    scopus 로고
    • Accurate design of megadalton-scale two-component icosahedral protein complexes
    • Bale JB, et al. (2016) Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 353:389–394.
    • (2016) Science , vol.353 , pp. 389-394
    • Bale, J.B.1
  • 16
    • 84982076183 scopus 로고    scopus 로고
    • Flexible, symmetry-directed approach to assembling protein cages
    • Sciore A, et al. (2016) Flexible, symmetry-directed approach to assembling protein cages. Proc Natl Acad Sci USA 113:8681–8686.
    • (2016) Proc Natl Acad Sci USA , vol.113 , pp. 8681-8686
    • Sciore, A.1
  • 17
    • 0042780350 scopus 로고    scopus 로고
    • Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins
    • Binz HK, Stumpp MT, Forrer P, Amstutz P, Plückthun A (2003) Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 332:489–503.
    • (2003) J Mol Biol , vol.332 , pp. 489-503
    • Binz, H.K.1    Stumpp, M.T.2    Forrer, P.3    Amstutz, P.4    Plückthun, A.5
  • 18
    • 49449118042 scopus 로고    scopus 로고
    • Light-activated DNA binding in a designed allosteric protein
    • Strickland D, Moffat K, Sosnick TR (2008) Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci USA 105:10709–10714.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 10709-10714
    • Strickland, D.1    Moffat, K.2    Sosnick, T.R.3
  • 19
    • 84855513111 scopus 로고    scopus 로고
    • Systematic control of protein interaction using a modular ER/K α-helix linker
    • Sivaramakrishnan S, Spudich JA (2011) Systematic control of protein interaction using a modular ER/K α-helix linker. Proc Natl Acad Sci USA 108:20467–20472.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 20467-20472
    • Sivaramakrishnan, S.1    Spudich, J.A.2
  • 20
    • 84962265255 scopus 로고    scopus 로고
    • DARPin-based crystallization chaperones exploit molecular geometry as a screening dimension in protein crystallography
    • Batyuk A, Wu Y, Honegger A, Heberling MM, Plückthun A (2016) DARPin-based crystallization chaperones exploit molecular geometry as a screening dimension in protein crystallography. J Mol Biol 428:1574–1588.
    • (2016) J Mol Biol , vol.428 , pp. 1574-1588
    • Batyuk, A.1    Wu, Y.2    Honegger, A.3    Heberling, M.M.4    Plückthun, A.5
  • 21
    • 84957709564 scopus 로고    scopus 로고
    • Generation of fluorogen-activating designed ankyrin repeat proteins (FADAs) as versatile sensor tools
    • Schütz M, et al. (2016) Generation of fluorogen-activating designed ankyrin repeat proteins (FADAs) as versatile sensor tools. J Mol Biol 428:1272–1289.
    • (2016) J Mol Biol , vol.428 , pp. 1272-1289
    • Schütz, M.1
  • 22
    • 85029379855 scopus 로고    scopus 로고
    • Rigidly connected multispecific artificial binders with adjustable geometries
    • Wu Y, et al. (2017) Rigidly connected multispecific artificial binders with adjustable geometries. Sci Rep 7:11217.
    • (2017) Sci Rep , vol.7 , pp. 11217
    • Wu, Y.1
  • 23
    • 21744440783 scopus 로고    scopus 로고
    • Intracellular kinase inhibitors selected from combinatorial libraries of designed ankyrin repeat proteins
    • Amstutz P, et al. (2005) Intracellular kinase inhibitors selected from combinatorial libraries of designed ankyrin repeat proteins. J Biol Chem 280:24715–24722.
    • (2005) J Biol Chem , vol.280 , pp. 24715-24722
    • Amstutz, P.1
  • 24
    • 71049152941 scopus 로고    scopus 로고
    • Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: Comparison of DARPin and camelid VHH binding mode
    • Veesler D, et al. (2009) Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: Comparison of DARPin and camelid VHH binding mode. J Biol Chem 284:30718–30726.
    • (2009) J Biol Chem , vol.284 , pp. 30718-30726
    • Veesler, D.1
  • 25
    • 84920848625 scopus 로고    scopus 로고
    • Designed ankyrin repeat proteins (DARPins): Binding proteins for research, diagnostics, and therapy
    • Plückthun A (2015) Designed ankyrin repeat proteins (DARPins): Binding proteins for research, diagnostics, and therapy. Annu Rev Pharmacol Toxicol 55:489–511.
    • (2015) Annu Rev Pharmacol Toxicol , vol.55 , pp. 489-511
    • Plückthun, A.1
  • 26
    • 53049085400 scopus 로고    scopus 로고
    • Chaperone-assisted crystallography with DARPins
    • Sennhauser G, Grütter MG (2008) Chaperone-assisted crystallography with DARPins. Structure 16:1443–1453.
    • (2008) Structure , vol.16 , pp. 1443-1453
    • Sennhauser, G.1    Grütter, M.G.2
  • 27
    • 85022322918 scopus 로고    scopus 로고
    • Electron cryo-microscopy structure of the mechanotransduction channel NOMPC
    • Jin P, et al. (2017) Electron cryo-microscopy structure of the mechanotransduction channel NOMPC. Nature 547:118–122.
    • (2017) Nature , vol.547 , pp. 118-122
    • Jin, P.1
  • 28
    • 77956176007 scopus 로고    scopus 로고
    • Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR
    • Wetzel SK, et al. (2010) Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR. J Mol Biol 402:241–258.
    • (2010) J Mol Biol , vol.402 , pp. 241-258
    • Wetzel, S.K.1
  • 29
    • 78349313323 scopus 로고    scopus 로고
    • Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned C-capping module
    • Kramer MA, Wetzel SK, Plückthun A, Mittl PRE, Grütter MG (2010) Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned C-capping module. J Mol Biol 404:381–391.
    • (2010) J Mol Biol , vol.404 , pp. 381-391
    • Kramer, M.A.1    Wetzel, S.K.2    Plückthun, A.3    Mittl, P.R.E.4    Grütter, M.G.5
  • 30
    • 84865302440 scopus 로고    scopus 로고
    • Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries
    • Kummer L, et al. (2012) Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries. Proc Natl Acad Sci USA 109:E2248–E2257.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. E2248-E2257
    • Kummer, L.1
  • 31
    • 84864343828 scopus 로고    scopus 로고
    • A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end
    • Pecqueur L, et al. (2012) A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end. Proc Natl Acad Sci USA 109:12011–12016.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 12011-12016
    • Pecqueur, L.1
  • 32
    • 84892930656 scopus 로고    scopus 로고
    • Design, construction, and characterization of a second-generation DARP in library with reduced hydrophobicity
    • Seeger MA, et al. (2013) Design, construction, and characterization of a second-generation DARP in library with reduced hydrophobicity. Protein Sci 22:1239–1257.
    • (2013) Protein Sci , vol.22 , pp. 1239-1257
    • Seeger, M.A.1
  • 33
    • 84981710085 scopus 로고    scopus 로고
    • Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein
    • Coscia F, et al. (2016) Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein. Sci Rep 6:30909.
    • (2016) Sci Rep , vol.6 , pp. 30909
    • Coscia, F.1
  • 34
    • 84911466782 scopus 로고    scopus 로고
    • Structure of a designed protein cage that self-assembles into a highly porous cube
    • Lai Y-T, et al. (2014) Structure of a designed protein cage that self-assembles into a highly porous cube. Nat Chem 6:1065–1071.
    • (2014) Nat Chem , vol.6 , pp. 1065-1071
    • Lai, Y.-T.1
  • 35
    • 84957074708 scopus 로고    scopus 로고
    • Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression
    • Bale JB, et al. (2015) Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression. Protein Sci 24:1695–1701.
    • (2015) Protein Sci , vol.24 , pp. 1695-1701
    • Bale, J.B.1
  • 37
    • 85014129582 scopus 로고    scopus 로고
    • MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy
    • Zheng SQ, et al. (2017) MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14:331–332.
    • (2017) Nat Methods , vol.14 , pp. 331-332
    • Zheng, S.Q.1
  • 38
    • 5144235316 scopus 로고    scopus 로고
    • XMIPP: A new generation of an open-source image processing package for electron microscopy
    • Sorzano CO, et al. (2004) XMIPP: A new generation of an open-source image processing package for electron microscopy. J Struct Biol 148:194–204.
    • (2004) J Struct Biol , vol.148 , pp. 194-204
    • Sorzano, C.O.1
  • 39
    • 84973518493 scopus 로고    scopus 로고
    • Processing of structurally heterogeneous cryo-EM data in RELION
    • Scheres SHW (2016) Processing of structurally heterogeneous cryo-EM data in RELION. Methods Enzymol 579:125–157.
    • (2016) Methods Enzymol , vol.579 , pp. 125-157
    • Scheres, S.H.W.1
  • 40
    • 84894623755 scopus 로고    scopus 로고
    • Quantifying the local resolution of cryo-EM density maps
    • Kucukelbir A, Sigworth FJ, Tagare HD (2014) Quantifying the local resolution of cryo-EM density maps. Nat Methods 11:63–65.
    • (2014) Nat Methods , vol.11 , pp. 63-65
    • Kucukelbir, A.1    Sigworth, F.J.2    Tagare, H.D.3
  • 41
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera–A visualization system for exploratory research and analysis
    • Pettersen EF, et al. (2004) UCSF Chimera–A visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612.
    • (2004) J Comput Chem , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1
  • 43
    • 84899803729 scopus 로고    scopus 로고
    • Relaxation of backbone bond geometry improves protein energy landscape modeling
    • Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D (2014) Relaxation of backbone bond geometry improves protein energy landscape modeling. Protein Sci 23:47–55.
    • (2014) Protein Sci , vol.23 , pp. 47-55
    • Conway, P.1    Tyka, M.D.2    DiMaio, F.3    Konerding, D.E.4    Baker, D.5
  • 44
    • 84996565974 scopus 로고    scopus 로고
    • Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
    • Wang RY-R, et al. (2016) Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5:e17219.
    • (2016) eLife , vol.5 , pp. e17219
    • Wang, R.Y.-R.1


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