Home LiteratureArticle Details
PMID: 27629640 Published · ppublish English Journal Article Review

Unravelling biological macromolecules with cryo-electron microscopy.

Nature ·Vol. 537 ·No. 7620 ·2016-00-15 ·Pages 339-46

Fernandez-Leiro R, Scheres SH

Abstract

Knowledge of the three-dimensional structures of proteins and other biological macromolecules often aids understanding of how they perform complicated tasks in the cell. Because many such tasks involve the cleavage or formation of chemical bonds, structural characterization at the atomic level is most useful. Developments in the electron microscopy of frozen hydrated samples (cryo-electron microscopy) are providing unprecedented opportunities for the structural characterization of biological macromolecules. This is resulting in a wave of information about processes in the cell that were impossible to characterize with existing techniques in structural biology.

MeSH Terms
Cryoelectron Microscopy/trends Humans Membrane Proteins/chemistry,ultrastructure Models, Molecular Multiprotein Complexes/chemistry,ultrastructure
Chemicals
Membrane Proteins Multiprotein Complexes
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Fernandez-Leiro Rafael
MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
Scheres Sjors H W
MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
References (120)
120 references, click to expand
  1. Structure of the yeast mitochondrial large ribosomal subunit.
    Science. 2014 Mar 28;343(6178):1485-9 PMID: 24675956
  2. Molecular architecture of the human U4/U6.U5 tri-snRNP.
    Science. 2016 Mar 25;351(6280):1416-20 PMID: 26912367
  3. Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.
    Nature. 2015 Jan 1;517(7532):50-5 PMID: 25517095
  4. Structure of the voltage-gated calcium channel Cav1.1 complex.
    Science. 2015 Dec 18;350(6267):aad2395 PMID: 26680202
  5. Atomic structure of the APC/C and its mechanism of protein ubiquitination.
    Nature. 2015 Jun 25;522(7557):450-4 PMID: 26083744
  6. Structural basis for retroviral integration into nucleosomes.
    Nature. 2015 Jul 16;523(7560):366-9 PMID: 26061770
  7. TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.
    Nature. 2016 May 18;534(7607):347-51 PMID: 27281200
  8. Structure of the eukaryotic MCM complex at 3.8 Å.
    Nature. 2015 Aug 13;524(7564):186-91 PMID: 26222030
  9. Structure- and function-based design of Plasmodium-selective proteasome inhibitors.
    Nature. 2016 Feb 11;530(7589):233-6 PMID: 26863983
  10. Cryo-EM single particle analysis with the Volta phase plate.
    Elife. 2016 Mar 07;5:null PMID: 26949259
  11. Acetylcholine receptor channel imaged in the open state.
    Nature. 1995 Jan 5;373(6509):37-43 PMID: 7800037
  12. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles.
    Elife. 2013 Feb 19;2:e00461 PMID: 23427024
  13. Beam-induced motion correction for sub-megadalton cryo-EM particles.
    Elife. 2014 Aug 13;3:e03665 PMID: 25122622
  14. Membrane protein assembly into Nanodiscs.
    FEBS Lett. 2010 May 3;584(9):1721-7 PMID: 19836392
  15. Trajectories of the ribosome as a Brownian nanomachine.
    Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17492-7 PMID: 25422471
  16. Structure and organization of heteromeric AMPA-type glutamate receptors.
    Science. 2016 Apr 29;352(6285):aad3873 PMID: 26966189
  17. Making membrane proteins for structures: a trillion tiny tweaks.
    Nat Methods. 2010 Jun;7(6):429-34 PMID: 20508636
  18. Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.
    Cell. 2015 Nov 19;163(5):1138-52 PMID: 26548953
  19. Architecture of mammalian respiratory complex I.
    Nature. 2014 Nov 6;515(7525):80-4 PMID: 25209663
  20. Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas.
    Nat Methods. 2014 Jun;11(6):649-52 PMID: 24747813
  21. Structure of the L Protein of Vesicular Stomatitis Virus from Electron Cryomicroscopy.
    Cell. 2015 Jul 16;162(2):314-27 PMID: 26144317
  22. Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle.
    Elife. 2016 Mar 31;5:null PMID: 27031283
  23. Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.
    Nature. 2015 Apr 23;520(7548):567-70 PMID: 25707802
  24. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.
    Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1867-72 PMID: 18238898
  25. ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.
    Cell. 2012 Mar 30;149(1):113-23 PMID: 22445172
  26. Visualizing the molecular sociology at the HeLa cell nuclear periphery.
    Science. 2016 Feb 26;351(6276):969-72 PMID: 26917770
  27. Transcription initiation complex structures elucidate DNA opening.
    Nature. 2016 May 11;533(7603):353-8 PMID: 27193681
  28. Structure of the human 26S proteasome at a resolution of 3.9 Å.
    Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):7816-21 PMID: 27342858
  29. Tor forms a dimer through an N-terminal helical solenoid with a complex topology.
    Nat Commun. 2016 Apr 13;7:11016 PMID: 27072897
  30. Electron diffraction of frozen, hydrated protein crystals.
    Science. 1974 Dec 13;186(4168):1036-7 PMID: 4469695
  31. Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.
    Elife. 2014 Feb 25;3:e01963 PMID: 24569482
  32. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
    Nat Methods. 2013 Jun;10(6):584-90 PMID: 23644547
  33. The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.
    Science. 2016 Jan 29;351(6272):466-75 PMID: 26743623
  34. Single particle electron cryomicroscopy: trends, issues and future perspective.
    Q Rev Biophys. 2016 Jan;49:e13 PMID: 27658821
  35. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.
    Elife. 2016 Nov 15;5:null PMID: 27845625
  36. Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6.
    Elife. 2015 May 29;4:e06980 PMID: 26023829
  37. cryo-EM structures of the E. coli replicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease and τ.
    Elife. 2015 Oct 24;4:null PMID: 26499492
  38. In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus.
    Nature. 2015 Nov 26;527(7579):531-4 PMID: 26503045
  39. Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
    Science. 2015 Apr 17;348(6232):303-8 PMID: 25837512
  40. Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy.
    Science. 2014 Dec 12;346(6215):1377-80 PMID: 25504723
  41. Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM.
    J Struct Biol. 2012 Jul;179(1):68-75 PMID: 22569522
  42. Graphene oxide: a substrate for optimizing preparations of frozen-hydrated samples.
    J Struct Biol. 2010 Apr;170(1):152-6 PMID: 20035878
  43. Computer averaging of electron micrographs of 40S ribosomal subunits.
    Science. 1981 Dec 18;214(4527):1353-5 PMID: 7313694
  44. Structural and biochemical basis for induced self-propagation of NLRC4.
    Science. 2015 Oct 23;350(6259):399-404 PMID: 26449475
  45. 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.
    Science. 2015 Jun 5;348(6239):1147-51 PMID: 25953817
  46. The cell as a collection of protein machines: preparing the next generation of molecular biologists.
    Cell. 1998 Feb 6;92(3):291-4 PMID: 9476889
  47. GTPase activation of elongation factor EF-Tu by the ribosome during decoding.
    EMBO J. 2009 Mar 18;28(6):755-65 PMID: 19229291
  48. Architecture and conformational switch mechanism of the ryanodine receptor.
    Nature. 2015 Jan 1;517(7532):39-43 PMID: 25470059
  49. Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation.
    Nat Struct Mol Biol. 2016 Mar;23(3):217-24 PMID: 26854665
  50. 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition.
    Science. 2016 Feb 19;351(6275):871-5 PMID: 26822609
  51. Structure of an RNA polymerase II preinitiation complex.
    Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13543-8 PMID: 26483468
  52. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.
    Structure. 2012 Nov 7;20(11):1823-8 PMID: 23022349
  53. Electron tomography: towards visualizing the molecular organization of the cytoplasm.
    Curr Opin Struct Biol. 2002 Oct;12(5):679-84 PMID: 12464323
  54. Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus.
    Science. 2015 Sep 18;349(6254):1347-50 PMID: 26383954
  55. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules.
    Q Rev Biophys. 1995 May;28(2):171-93 PMID: 7568675
  56. Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud.
    Elife. 2015 May 08;4:null PMID: 25955969
  57. A national facility for biological cryo-electron microscopy.
    Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):127-35 PMID: 25615867
  58. Biochemistry. The resolution revolution.
    Science. 2014 Mar 28;343(6178):1443-4 PMID: 24675944
  59. Near-atomic resolution reconstructions using a mid-range electron microscope operated at 200 kV.
    J Struct Biol. 2014 Nov;188(2):183-7 PMID: 25278130
  60. Ribosome. The structure of the human mitochondrial ribosome.
    Science. 2015 Apr 3;348(6230):95-8 PMID: 25838379
  61. Gating machinery of InsP3R channels revealed by electron cryomicroscopy.
    Nature. 2015 Nov 19;527(7578):336-41 PMID: 26458101
  62. Architecture of human mTOR complex 1.
    Science. 2016 Jan 1;351(6268):48-52 PMID: 26678875
  63. Mechanistic insights into the recycling machine of the SNARE complex.
    Nature. 2015 Feb 5;518(7537):61-7 PMID: 25581794
  64. Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.
    Nature. 2016 May 02;534(7605):63-8 PMID: 27135925
  65. Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution.
    Nature. 2016 May 18;534(7605):69-74 PMID: 27251276
  66. A saposin-lipoprotein nanoparticle system for membrane proteins.
    Nat Methods. 2016 Apr;13(4):345-51 PMID: 26950744
  67. Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer.
    Science. 2016 Mar 4;351(6277):1043-8 PMID: 26941313
  68. Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase.
    Science. 2016 Jun 24;352(6293):1542-7 PMID: 27339980
  69. Structural mechanism of glutamate receptor activation and desensitization.
    Nature. 2014 Oct 16;514(7522):328-34 PMID: 25119039
  70. 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy.
    Elife. 2015 Mar 11;4:null PMID: 25760083
  71. TRPV1 structures in distinct conformations reveal activation mechanisms.
    Nature. 2013 Dec 5;504(7478):113-8 PMID: 24305161
  72. Enhanced imaging in low dose electron microscopy using electron counting.
    Ultramicroscopy. 2009 Nov;109(12):1411-6 PMID: 19647366
  73. Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1.
    EMBO J. 2011 Sep 09;30(22):4652-64 PMID: 21909073
  74. 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
    Nature. 2008 May 15;453(7193):415-9 PMID: 18449192
  75. Structural snapshots of actively translating human ribosomes.
    Cell. 2015 May 7;161(4):845-57 PMID: 25957688
  76. Molecular mechanism of APC/C activation by mitotic phosphorylation.
    Nature. 2016 Apr 27;533(7602):260-4 PMID: 27120157
  77. Leginon: a system for fully automated acquisition of 1000 electron micrographs a day.
    Ultramicroscopy. 1999 Jul;77(3-4):153-61 PMID: 10406132
  78. Structural insight into nascent polypeptide chain-mediated translational stalling.
    Science. 2009 Dec 4;326(5958):1412-5 PMID: 19933110
  79. Likelihood-based classification of cryo-EM images using FREALIGN.
    J Struct Biol. 2013 Sep;183(3):377-88 PMID: 23872434
  80. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.
    Nat Methods. 2007 Jan;4(1):27-9 PMID: 17179934
  81. Horizontal membrane-intrinsic α-helices in the stator a-subunit of an F-type ATP synthase.
    Nature. 2015 May 14;521(7551):237-40 PMID: 25707805
  82. Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection.
    Cell. 2016 Jun 2;165(6):1467-78 PMID: 27238017
  83. Molecular architecture of the inner ring scaffold of the human nuclear pore complex.
    Science. 2016 Apr 15;352(6283):363-5 PMID: 27081072
  84. Parallel, distributed and GPU computing technologies in single-particle electron microscopy.
    Acta Crystallogr D Biol Crystallogr. 2009 Jul;65(Pt 7):659-71 PMID: 19564686
  85. Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning.
    Science. 2015 May 1;348(6234):581-5 PMID: 25837515
  86. An atomic structure of human γ-secretase.
    Nature. 2015 Sep 10;525(7568):212-7 PMID: 26280335
  87. Mechanism of NMDA Receptor Inhibition and Activation.
    Cell. 2016 Apr 21;165(3):704-14 PMID: 27062927
  88. Structure of a group II intron in complex with its reverse transcriptase.
    Nat Struct Mol Biol. 2016 Jun;23 (6):549-57 PMID: 27136327
  89. Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.
    Elife. 2016 Jan 08;5:e13027 PMID: 26744777
  90. Near-atomic resolution visualization of human transcription promoter opening.
    Nature. 2016 May 11;533(7603):359-65 PMID: 27193682
  91. Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
    Nature. 2016 Feb 18;530(7590):298-302 PMID: 26829225
  92. Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
    Nature. 2013 Dec 5;504(7478):107-12 PMID: 24305160
  93. Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy.
    Ultramicroscopy. 2014 Dec;147:156-63 PMID: 25194828
  94. Cryo-EM structure of SNAP-SNARE assembly in 20S particle.
    Cell Res. 2015 May;25(5):551-60 PMID: 25906996
  95. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.
    Science. 2014 Apr 25;344(6182):376-80 PMID: 24763583
  96. Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome.
    Nature. 2016 Mar 31;531(7596):598-603 PMID: 27029275
  97. Generalized single-particle cryo-EM--a historical perspective.
    Microscopy (Oxf). 2016 Feb;65(1):3-8 PMID: 26566976
  98. Structure of a mammalian ryanodine receptor.
    Nature. 2015 Jan 1;517(7532):44-9 PMID: 25470061
  99. Molecular structures of unbound and transcribing RNA polymerase III.
    Nature. 2015 Dec 10;528(7581):231-6 PMID: 26605533
  100. Detective quantum efficiency of electron area detectors in electron microscopy.
    Ultramicroscopy. 2009 Aug;109(9):1126-43 PMID: 19497671
  101. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
    Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1063-8 PMID: 19122150
  102. Glycine receptor mechanism elucidated by electron cryo-microscopy.
    Nature. 2015 Oct 8;526(7572):224-9 PMID: 26344198
  103. CryoEM structure of yeast cytoplasmic exosome complex.
    Cell Res. 2016 Jul;26(7):822-37 PMID: 27174052
  104. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.
    Science. 2015 Oct 23;350(6259):404-9 PMID: 26449474
  105. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function.
    Nature. 2016 Feb 18;530(7590):358-61 PMID: 26887496
  106. The structure of the dynactin complex and its interaction with dynein.
    Science. 2015 Mar 27;347(6229):1441-6 PMID: 25814576
  107. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy.
    Structure. 2015 Jun 2;23(6):1097-105 PMID: 26004440
  108. Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase.
    Nature. 2015 May 14;521(7551):241-5 PMID: 25971514
  109. Structural organization of the dynein-dynactin complex bound to microtubules.
    Nat Struct Mol Biol. 2015 Apr;22(4):345-7 PMID: 25751425
  110. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.
    Science. 2016 Feb 19;351(6275):867-71 PMID: 26841432
  111. A Bayesian view on cryo-EM structure determination.
    J Mol Biol. 2012 Jan 13;415(2):406-18 PMID: 22100448
  112. Cryo-electron microscopy structure of the Slo2.2 Na(+)-activated K(+) channel.
    Nature. 2015 Nov 12;527(7577):198-203 PMID: 26436452
  113. Structure of transcribing mammalian RNA polymerase II.
    Nature. 2016 Jan 28;529(7587):551-4 PMID: 26789250
  114. Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.
    Cell. 2016 Jun 16;165(7):1698-707 PMID: 27238019
  115. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer.
    Science. 2013 Dec 20;342(6165):1484-90 PMID: 24179160
  116. A maximum-likelihood approach to single-particle image refinement.
    J Struct Biol. 1998;122(3):328-39 PMID: 9774537
  117. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy.
    Nature. 2008 Feb 28;451(7182):1130-4 PMID: 18305544
  118. Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate.
    Nat Commun. 2016 Feb 18;7:10708 PMID: 26888060
  119. Beam-induced motion of vitrified specimen on holey carbon film.
    J Struct Biol. 2012 Mar;177(3):630-7 PMID: 22366277
  120. Structural and molecular basis for Ebola virus neutralization by protective human antibodies.
    Science. 2016 Mar 18;351(6279):1343-6 PMID: 26917592
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2016-00-15
Pages
339-46
Language
English
Region
England
NLM ID
0410462
PMCID
PMC5074357
Subset
IM
Grants
Medical Research Council · MC_U105197143 · United Kingdom
Medical Research Council · MC_UP_A025_1013 · United Kingdom
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com