Foundational literature & more
Literature resources for foundational knowledge.
Start with the top list of curated papers. Are you also interested in what papers we have done for journal club? Then look at the papers our staff have found interesting.
Seminal papers
A good starting point.
- A primer to single-particle cryo-electron microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/25910204 - Visualizing molecular machines in action: Single-particle analysis with structural variability:
https://www.ncbi.nlm.nih.gov/pubmed/21115174 - Visualizing proteins and macromolecular complexes by negative stain EM: from grid preparation to image acquisition:
https://www.ncbi.nlm.nih.gov/pubmed/22215030 - Structural analysis of macromolecular assemblies by electron microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/21919528 - Structural analysis of supramolecular assemblies by cryo-electron tomography:
https://www.ncbi.nlm.nih.gov/pubmed/24010711 - High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles:
https://www.ncbi.nlm.nih.gov/pubmed/24390311 - Realizing the potential of electron cryo-microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/17390603 - Towards a mechanistic understanding of cellular processes by cryoEM:
https://www.ncbi.nlm.nih.gov/pubmed/31349128 - Membrane mimetic systems in CryoEM: keeping membrane proteins in their native environment:
https://www.ncbi.nlm.nih.gov/pubmed/31279500 - CryoEM: a crystals to single particles round-trip:
https://www.ncbi.nlm.nih.gov/pubmed/31233976 - The cryo-EM method microcrystal electron diffraction (MicroED):
https://www.ncbi.nlm.nih.gov/pubmed/31040436 - Challenges and opportunities in cryo-EM single-particle analysis:
https://www.ncbi.nlm.nih.gov/pubmed/30804214 - Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis:
https://www.ncbi.nlm.nih.gov/pubmed/30793729 - Cellular and Structural Studies of Eukaryotic Cells by Cryo-Electron Tomography:
https://www.ncbi.nlm.nih.gov/pubmed/30654455 - Cryo-EM in drug discovery:
https://www.ncbi.nlm.nih.gov/pubmed/30647139 - Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age:
https://www.ncbi.nlm.nih.gov/pubmed/30605120 - Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead:
https://www.ncbi.nlm.nih.gov/pubmed/30509756 - Electron tomography in plant cell biology:
https://www.ncbi.nlm.nih.gov/pubmed/30452668 - Unravelling molecular complexity in structural cell biology:
https://www.ncbi.nlm.nih.gov/pubmed/30339965 - Cryo-EM (in general):
https://www.ncbi.nlm.nih.gov/pubmed/30300591 - Biological Applications at the Cutting Edge of Cryo-Electron Microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/30175702 - Single-particle cryo-EM-How did it get here and where will it go:
https://www.ncbi.nlm.nih.gov/pubmed/30166484 - Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy
https://www.ncbi.nlm.nih.gov/pubmed/14568533 - What Could Go Wrong? A Practical Guide To Single-Particle Cryo-EM: From Biochemistry To Atomic Models
https://www.ncbi.nlm.nih.gov/pubmed/32078321 - A good primer on what the .mrc file format is: MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography
https://www.ncbi.nlm.nih.gov/pubmed/25882513
Journal club papers
Topics of interest to the staff from the past 2 years, in no particular order.
Methods
- Averaging of low exposure electron micrographs of non-periodic objects:
https://www.ncbi.nlm.nih.gov/pubmed/1236029 - Microscale Fluid Behavior during Cryo-EM Sample Blotting:
https://www.ncbi.nlm.nih.gov/pubmed/31952802 - A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue:
https://www.ncbi.nlm.nih.gov/pubmed/31363205 - PIE-scope, integrated cryo-correlative light and FIB/SEM microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/31259689 - Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device:
https://www.ncbi.nlm.nih.gov/pubmed/31793900 - Mind the gap: Micro-expansion joints drastically decrease the bending of FIB-milled cryo-lamellae:
https://www.ncbi.nlm.nih.gov/pubmed/31536774 - How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?:
https://www.ncbi.nlm.nih.gov/pubmed/30786229 - Microfluidic protein isolation and sample preparation for high-resolution cryo-EMMicrofluidic protein isolation and sample preparation for high-resolution cryo-EM:
https://www.ncbi.nlm.nih.gov/pubmed/31292253 - A cryo-EM grid preparation device for time-resolved structural studies:
https://www.ncbi.nlm.nih.gov/pubmed/31709058 - Real-space refinement in PHENIX for cryo-EM and crystallography:
https://www.ncbi.nlm.nih.gov/pubmed/29872004 - Real-time cryo-electron microscopy data preprocessing with Warp:
https://www.ncbi.nlm.nih.gov/pubmed/31591575 - A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality:
https://www.ncbi.nlm.nih.gov/pubmed/30449687 - Averaging of low exposure electron micrographs of non-periodic objects:
https://www.ncbi.nlm.nih.gov/pubmed/1236029
.
Application
- The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus:
https://www.ncbi.nlm.nih.gov/pubmed/28959035 - A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/28959045 - An allosteric mechanism for potent inhibition of human ATP-citrate lyase:
https://www.ncbi.nlm.nih.gov/pubmed/30944472 - Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution:
https://www.ncbi.nlm.nih.gov/pubmed/31160591 - Reduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps:
https://www.ncbi.nlm.nih.gov/pubmed/30260634 - Structure of the human MHC-I peptide-loading complex:
https://www.ncbi.nlm.nih.gov/pubmed/29107940 - Complement is activated by IgG hexamers assembled at the cell surface:
https://www.ncbi.nlm.nih.gov/pubmed/24626930 - Revisiting the Structure of Hemoglobin and Myoglobin with Cryo-Electron Microscopy:
https://www.ncbi.nlm.nih.gov/pubmed/28697886 - Cryo-EM structure of a human spliceosome activated for step 2 of splicing:
https://www.ncbi.nlm.nih.gov/pubmed/28076346 - Cryo-EM Structure of the Open Human Ether-à-go-go-Related K+ Channel hERG:
https://www.ncbi.nlm.nih.gov/pubmed/28431243 - Visualizing the molecular sociology at the HeLa cell nuclear periphery:
https://www.ncbi.nlm.nih.gov/pubmed/26917770 - Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator:
https://www.ncbi.nlm.nih.gov/pubmed/27912062 - Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery:
https://www.ncbi.nlm.nih.gov/pubmed/27238019 - Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate:
https://www.ncbi.nlm.nih.gov/pubmed/28665412 - Sampling the conformational space of the catalytic subunit of human γ-secretase:
https://www.ncbi.nlm.nih.gov/pubmed/26623517 - Lipid–protein interactions in double-layered two-dimensional AQP0 crystals:
https://www.ncbi.nlm.nih.gov/pubmed/16319884
Support film references
In our experience, preparing grids with an added graphene or graphene oxide layer is difficult to do in-house reproducibly. Commercially available grids, however, are not consistently better, so we often still prepare these grids ourselves.
Attention to every single detail is key to reproducibility. Therefore, we recommend using the references below as a foundational guide for developing your own protocol for your exact reagents, available instrumentation, and hands. We generally make 1-2 grids following a given protocol and inspect the dry grids by TEM (at room temp) until we have adequate (note: it is never perfect!) area of clean support film before scaling up.
We have used the following references as a guide. This is not a comprehensive reference list, but our favorite generally-accessible and easy-to-follow protocols.
Methods
Graphene
- High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy:
https://pubmed.ncbi.nlm.nih.gov/31879346/ - Materials from our 2021 workshop, including a protocol with product catalog numbers (find “workshop worksheet” link) can be found on our workshop archive:
https://nccat.nysbc.org/activities/graphene-workshop-2021/
Graphene oxide
- Efficient graphene oxide coating improves cryo-EM sample preparation and data collection from tilted grids:
https://www.biorxiv.org/content/10.1101/2021.03.08.434344v1 - Simplified Approach for Preparing Graphene Oxide TEM Grids for Stained and Vitrified Biomolecules:
https://pubmed.ncbi.nlm.nih.gov/33808009/ - A simple and robust procedure for preparing graphene-oxide cryo-EM grids:
https://pubmed.ncbi.nlm.nih.gov/30017701/ - Graphene Oxide Grid Preparation. Protocol and practical demonstration recording from the Scheres Group:
Video hosted at Figshare
Reviews on the topic of support films in cryoEM
- Proteins, Interfaces, and Cryo-EM Grids:
https://pubmed.ncbi.nlm.nih.gov/29867291/ - Application of Monolayer Graphene and Its Derivative in Cryo-EM Sample Preparation:
https://pubmed.ncbi.nlm.nih.gov/34445650/ - Graphene in cryo-EM specimen optimization:
https://pubmed.ncbi.nlm.nih.gov/38688075/