Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution.

Cryoelectron Microscopy / methods Signal-To-Noise Ratio Microscopy, Electron, Scanning Transmission / methods Imaging, Three-Dimensional / methods Apoferritins / chemistry Proteins / chemistry Image Processing, Computer-Assisted / methods

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
14 Sep 2024
Historique:
received: 10 03 2024
accepted: 05 09 2024
medline: 15 9 2024
pubmed: 15 9 2024
entrez: 14 9 2024
Statut: epublish

Résumé

Cryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography - a coherent diffractive imaging technique using 4D scanning transmission electron microscopy (4D-STEM) - has recently demonstrated excellent SNR and resolution down to tens of picometers for thin specimens imaged at room temperature. Here we apply 4D-STEM and ptychographic data analysis to frozen hydrated proteins, reaching sub-nanometer resolution 3D reconstructions. We employ low-dose cryo-EM with an aberration-corrected, convergent electron beam to collect 4D-STEM data for our reconstructions. The high frame rate of the electron detector allows us to record large datasets of electron diffraction patterns with substantial overlaps between the interaction volumes of adjacent scan positions, from which the scattering potentials of the samples are iteratively reconstructed. The reconstructed micrographs show strong SNR enabling the reconstruction of the structure of apoferritin protein at up to 5.8 Å resolution. We also show structural analysis of the Phi92 capsid and sheath, tobacco mosaic virus, and bacteriorhodopsin at slightly lower resolutions.

Identifiants

DOI: 10.1038/s41467-024-52403-5 PMID: 39277607
pubmed: 39277607
doi: 10.1038/s41467-024-52403-5
pii: 10.1038/s41467-024-52403-5
doi:

Substances chimiques

Apoferritins 9013-31-4
Proteins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

8062

Subventions

Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
ID : 200021_200628
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)
ID : 101118656
Organisme : DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
ID : DE-AC02-05CH11231

Informations de copyright

© 2024. The Author(s).

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Auteurs

Berk Küçükoğlu (B)

Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.

Inayathulla Mohammed (I)

Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.

Ricardo C Guerrero-Ferreira (RC)

Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.
Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA.
ORCID: 0000-0002-3664-8277

Stephanie M Ribet (SM)

National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Georgios Varnavides (G)

National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA.
ORCID: 0000-0001-8338-3323

Max Leo Leidl (ML)

Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.
Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Butenandstr. 11, 81377, München, Germany.
ORCID: 0000-0001-8896-1647

Kelvin Lau (K)

Protein Production and Structure Core Facility (PTPSP), School of Life Sciences, EPFL, Rte Cantonale, 1015, Lausanne, Switzerland.
ORCID: 0000-0002-9040-7597

Sergey Nazarov (S)

Dubochet Center for Imaging Lausanne, EPFL and UNIL, EPFL VPA DCI-Lausanne, 1015, Lausanne, Switzerland.

Alexander Myasnikov (A)

Dubochet Center for Imaging Lausanne, EPFL and UNIL, EPFL VPA DCI-Lausanne, 1015, Lausanne, Switzerland.
ORCID: 0000-0003-2607-7121

Massimo Kube (M)

Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.

Julika Radecke (J)

Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.

Carsten Sachse (C)

Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.
Department of Biology, Heinrich Heine University, Düsseldorf, Germany.
ORCID: 0000-0002-1168-5143

Knut Müller-Caspary (K)

Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Butenandstr. 11, 81377, München, Germany.
ORCID: 0000-0002-2588-7993

Colin Ophus (C)

National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0003-2348-8558

Henning Stahlberg (H)

Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland. henning.stahlberg@epfl.ch.
ORCID: 0000-0002-1185-4592

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Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Microscopie électronique › Cryomicroscopie électronique › Low-dose cryo-electron ptychography of...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Sensibilité et spécificité › Rapport signal-bruit › Low-dose cryo-electron ptychography of...
questionsmedicales.fr › Techniques d'investigation › Microscopie électronique › Microscopie électronique à transmission › Microscopie électronique en transmission à balayage › Low-dose cryo-electron ptychography of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Traitement d'image par ordinateur › Imagerie tridimensionnelle › Low-dose cryo-electron ptychography of...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Métalloprotéines › Protéines de liaison au fer › Ferritines › Apoferritines › Low-dose cryo-electron ptychography of...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Low-dose cryo-electron ptychography of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Traitement d'image par ordinateur › Low-dose cryo-electron ptychography of...