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Nievergelt P, Berliat F, McAuley KE, Dorgan CR, van Well RM, Thorn A, Spingler B. RNA oligomers at atomic resolution containing 1-methylpseudouridine, an essential building block of mRNA vaccines. ChemMedChem 2024; 19:e202300600. [PMID: 38235959 DOI: 10.1002/cmdc.202300600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
All widely used mRNA vaccines against COVID-19 contain in their sequence 1-methylpseudouridine (m1Ψ) instead of uridine. In this publication, we report two high resolution crystal structures (at up to 1.01 and 1.32 Å, respectively) of one such double-stranded 12-mer RNA sequence crystallized in two crystal forms. The structures are compared with similar structures which do not contain this modification. Additionally, the X-ray structure of 1-methyl-pseudouridine itself was determined.
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Affiliation(s)
- Philipp Nievergelt
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Florian Berliat
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | | | - Colin R Dorgan
- Biosynth Limited, Compton, Berkshire, RG20 6NE, United Kingdom
| | | | - Andrea Thorn
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, 22761, Hamburg, Germany
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
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2
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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller WJ, Förster F. Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells. Mol Cell 2024; 84:1078-1089.e4. [PMID: 38340715 PMCID: PMC7615912 DOI: 10.1016/j.molcel.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/06/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA; Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA; Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
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3
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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4
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Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie 2024; 217:20-30. [PMID: 37741547 DOI: 10.1016/j.biochi.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.
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Affiliation(s)
- Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France.
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5
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Kazan R, Bourgeois G, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Structural insights into the evolution of late steps of translation initiation in the three domains of life. Biochimie 2024; 217:31-41. [PMID: 36773835 DOI: 10.1016/j.biochi.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. These two factors are also orthologous to the bacterial IF2 and IF1 proteins, respectively. Recent cryo-EM studies showed how e/aIF5B and e/aIF1A cooperate on the small ribosomal subunit to favor the binding of the large ribosomal subunit and the formation of a ribosome competent for elongation. In this review, pioneering studies and recent biochemical and structural results providing new insights into the role of a/eIF5B in archaea and eukaryotes will be presented. Recent structures will also be compared to orthologous bacterial initiation complexes to highlight domain-specific features and the evolution of initiation mechanisms.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
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6
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Uday AB, Mishra RK, Hussain T. Initiation factor 3 bound to the 30S ribosomal subunit in an initial step of translation. Proteins 2023. [PMID: 38148682 DOI: 10.1002/prot.26655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Bacterial ribosomes require three initiation factors IF1, IF2, and IF3 during the initial steps of translation. These IFs ensure correct base pairing of the initiator tRNA anticodon with the start codon in the mRNA located at the P-site of the 30S ribosomal subunit. IF3 is one of the first IFs to bind to the 30S and plays a crucial role in the selection of the correct start codon and codon: anticodon base pairing. IF3 also prevents the premature association of the 50S subunit of ribosomes and aids in ribosome recycling. IF3 is reported to change binding sites and conformation to ensure translation initiation fidelity. A recent study suggested an initial binding of IF3 CTD away from the P-site and that IF1 and IF2 promote the movement of CTD to the P-site and concomitant movement of NTD. Hence, to visualize the position of IF3 in the absence of any other IFs, we determined cryo-EM structure of the 30S-IF3 complex. The map shows that IF3 is present in an extended conformation with CTD present at the P-site and NTD near the platform even in the absence of IF1 and IF2. Hence, IF3 CTD binds at the P-site and moves away during the accommodation of the initiator tRNA at the P-site in the later steps of translation initiation. Overall, we report the structure of 30S-IF3 which demystifies the starting binding site and conformation of IF3 on the 30S ribosomal subunit.
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Affiliation(s)
- Adwaith B Uday
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
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Wang YH, Dai H, Zhang L, Wu Y, Wang J, Wang C, Xu CH, Hou H, Yang B, Zhu Y, Zhang X, Zhou J. Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome. Nucleic Acids Res 2023; 51:8909-8924. [PMID: 37604686 PMCID: PMC10516650 DOI: 10.1093/nar/gkad661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/29/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
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Affiliation(s)
- Ying-Hui Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hong Dai
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ling Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yun Wu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jingfen Wang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chen Wang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Cai-Huang Xu
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Hai Hou
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yongqun Zhu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xing Zhang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Zhou
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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8
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Westhof E, Watson ZL, Zirbel CL, Cate JHD. Anionic G•U pairs in bacterial ribosomal rRNAs. RNA (NEW YORK, N.Y.) 2023; 29:1069-1076. [PMID: 37068913 DOI: 10.1261/rna.079583.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/05/2023] [Indexed: 06/18/2023]
Abstract
Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson-Crick pairs. Another type of G•U pair interacting via their Watson-Crick edges has been observed in the A site of ribosome structures between a modified U34 in the tRNA anticodon triplet and G + 3 in the mRNA. In such pairs, the electronic structure of the U is changed with a negative charge on N3(U), resulting in two H-bonds between N1(G)…O4(U) and N2(G)…N3(U). Here, we report that such pairs occur in other highly conserved positions in ribosomal RNAs of bacteria in the absence of U modification. An anionic cis Watson-Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions.
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Affiliation(s)
- Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, F-67084 Strasbourg, France
| | - Zoe L Watson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
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9
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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller W, Förster F. Visualization of translation reorganization upon persistent collision stress in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533914. [PMID: 36993420 PMCID: PMC10055323 DOI: 10.1101/2023.03.23.533914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Aberrantly slow mRNA translation leads to ribosome stalling and subsequent collision with the trailing neighbor. Ribosome collisions have recently been shown to act as stress sensors in the cell, with the ability to trigger stress responses balancing survival and apoptotic cell-fate decisions depending on the stress level. However, we lack a molecular understanding of the reorganization of translation processes over time in mammalian cells exposed to an unresolved collision stress. Here we visualize the effect of a persistent collision stress on translation using in situ cryo electron tomography. We observe that low dose anisomycin collision stress leads to the stabilization of Z-site bound tRNA on elongating 80S ribosomes, as well as to the accumulation of an off-pathway 80S complex possibly resulting from collision splitting events. We visualize collided disomes in situ, occurring on compressed polysomes and revealing a stabilized geometry involving the Z-tRNA and L1 stalk on the stalled ribosome, and eEF2 bound to its collided rotated-2 neighbor. In addition, non-functional post-splitting 60S complexes accumulate in the stressed cells, indicating a limiting Ribosome associated Quality Control clearing rate. Finally, we observe the apparition of tRNA-bound aberrant 40S complexes shifting with the stress timepoint, suggesting a succession of different initiation inhibition mechanisms over time. Altogether, our work visualizes the changes of translation complexes under persistent collision stress in mammalian cells, indicating how perturbations in initiation, elongation and quality control processes contribute to an overall reduced protein synthesis.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
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10
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Kazan R, Bourgeois G, Carisetti D, Florea I, Larquet E, Maurice JL, Mechulam Y, Ozanam F, Schmitt E, Coureux PD. Grid batch-dependent tuning of glow discharge parameters. Front Mol Biosci 2022; 9:910218. [PMID: 36060254 PMCID: PMC9436422 DOI: 10.3389/fmolb.2022.910218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Sample preparation on cryo-EM grids can give various results, from very thin ice and homogeneous particle distribution (ideal case) to unwanted behavior such as particles around the “holes” or complexes that do not entirely correspond to the one in solution (real life). We recently run into such a case and finally found out that variations in the 3D reconstructions were systematically correlated with the grid batches that were used. We report the use of several techniques to investigate the grids' characteristics, namely TEM, SEM, Auger spectroscopy and Infrared Interferometry. This allowed us to diagnose the origin of grid preparation problems and to adjust glow discharge parameters. The methods used for each approach are described and the results obtained on a common specific case are reported.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | | | - Ileana Florea
- Laboratoire de Physique des Interfaces et Couches Minces (LPICM), CNRS-UMR 7647, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, Palaiseau, France
| | - Jean-Luc Maurice
- Laboratoire de Physique des Interfaces et Couches Minces (LPICM), CNRS-UMR 7647, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | - François Ozanam
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
- *Correspondence: Pierre-Damien Coureux,
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