Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells.
Journal, issue, pages	Nat Methods, Vol. 18, Issue 2, Page 186-193, Year 2021
Publish date	Feb 4, 2021
Authors	Dimitry Tegunov / Liang Xue / Christian Dienemann / Patrick Cramer / Julia Mahamid /
PubMed Abstract	Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and ...Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.
External links	Nat Methods / PubMed:33542511 / PubMed Central
Methods	EM (subtomogram averaging) / EM (single particle)
Resolution	1.34 - 6.0 Å
Structure data	EMDB-11603: Human heavy-chain apoferritin refined from tilt series data using M Method: EM (subtomogram averaging) / Resolution: 2.3 Å EMDB-11611: Human heavy-chain apoferritin refined from frame series data using M Method: EM (single particle) / Resolution: 2.3 Å EMDB-11650: M. pneumoniae 70S ribosome in complex with chloramphenicol obtained from in situ data using M Method: EM (subtomogram averaging) / Resolution: 3.5 Å EMDB-11651: SARS-CoV-2 spike protein obtained from EMPIAR-10453 using M Method: EM (subtomogram averaging) / Resolution: 3.8 Å EMDB-11652: Apoferritin obtained from EMPIAR-10248 using M Method: EM (single particle) / Resolution: 1.34 Å EMDB-11653: 80S ribosome obtained from EMPIAR-10045 using M Method: EM (subtomogram averaging) / Resolution: 6.0 Å EMDB-11654: 80S ribosome obtained from EMPIAR-10064 using M Method: EM (subtomogram averaging) / Resolution: 5.7 Å EMDB-11655: HIV-1 capsid-SP1 obtained from EMPIAR-10164 using M Method: EM (subtomogram averaging) / Resolution: 3.0 Å EMDB-11656: Cannabinoid Receptor 1-G obtained from EMPIAR-10288 using M Method: EM (single particle) / Resolution: 2.9 Å EMDB-11998: M. pneumoniae 70S ribosome in complex with chloramphenicol obtained from in situ data using M, focused refinement of 30S sub-unit Method: EM (subtomogram averaging) / Resolution: 3.7 Å EMDB-11999: M. pneumoniae 70S ribosome in complex with chloramphenicol obtained from in situ data using M, focused refinement of 50S sub-unit Method: EM (subtomogram averaging) / Resolution: 3.4 Å
Source	Homo sapiens (human) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Mus musculus (house mouse) Saccharomyces cerevisiae (brewer's yeast) Oryctolagus cuniculus (rabbit)