Automatic local resolution-based sharpening of cryo-EM maps

Ramírez-Aportela, Erney; Vilas, José Luis; Melero, Roberto; Conesa, Pablo; Martínez, Marta; Maluenda, David; Mota, Javier; Jiménez, Álvaro; Vargas, Javier; Marabini, Roberto; Carazo, José Marı́a; Sorzano, C.O.S.

doi:10.1101/433284

Cited by 21 publications

(16 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Extracted particles were imported into cryoSPARC v2.12.4 (15) for 2D classification, 3D 159 classification and non-uniform 3D refinement. The C1 RBD "up" reconstruction was sharpened 160 in cryoSPARC, and the 3D reconstruction with C3 symmetry was subjected to local B-factor 161 sharpening using LocalDeBlur (33). Models were built in Coot, before being iteratively refined 162 in both Phenix and ISOLDE (34)(35)(36).…”

Section: Cryo-em Data Processing 157mentioning

confidence: 99%

Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation

Wrapp

Wang

Corbett

et al. 2020

Preprint

1,351

1,910

View full text Add to dashboard Cite

1The outbreak of a novel betacoronavirus (2019-nCov) represents a pandemic threat that has been 2 declared a public health emergency of international concern. The CoV spike (S) glycoprotein is a 3 key target for urgently needed vaccines, therapeutic antibodies, and diagnostics. To facilitate 4 medical countermeasure (MCM) development we determined a 3.5 Å-resolution cryo-EM 5 structure of the 2019-nCoV S trimer in the prefusion conformation. The predominant state of the 6 trimer has one of the three receptor-binding domains (RBDs) rotated up in a receptor-accessible 7 conformation. We also show biophysical and structural evidence that the 2019-nCoV S binds 8 ACE2 with higher affinity than SARS-CoV S. Additionally we tested several published SARS-9CoV RBD-specific monoclonal antibodies and found that they do not have appreciable binding to 10 nCoV-2019 S, suggesting antibody cross-reactivity may be limited between the two virus RBDs. 11The atomic-resolution structure of 2019-nCoV S should enable rapid development and evaluation

show abstract

Section: Cryo-em Data Processing 157mentioning

confidence: 99%

Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation

Wrapp

Wang

Corbett

et al. 2020

Preprint

1,351

1,910

View full text Add to dashboard Cite

show abstract

“…Often times, especially for large assemblies, some of the most interesting biology occurs in the outer segments of a map, whereby auxiliary (often sub-stoichiometrically occupied) components or associated protein factors relay a signal to the catalytic core (190). The proper way to interpret such structural cascades is through a careful assessment of local resolution and of locally filtered maps (188,191). Local resolution…”

Section: Cryo-em Map and Atomic Model Validationmentioning

confidence: 99%

Challenges and opportunities in cryo-EM single-particle analysis

Lyumkis

2019

Journal of Biological Chemistry

312

235

View full text Add to dashboard Cite

Edited by Karin Musier-Forsyth Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.

show abstract

“…Using Relion post-processing, we were able to determine the overall reconstruction resolution to be 4 Å ( Figure S1). Local resolution was determined using the corresponding Relion tool and local sharpening was done using LocalDeblur 37 . Over-sharpening was seen in last iterations of local sharpening.…”

Section: Image Processingmentioning

confidence: 99%

Distinct cryo-EM Structure of α-synuclein Filaments derived by Tau

Hojjatian

Dasari

Sengupta

et al. 2021

Preprint

View full text Add to dashboard Cite

Recent structural studies of ex vivo amyloid filaments extracted from human patients demonstrated that the ex vivo filaments associated with different disease phenotypes adopt diverse molecular conformations distinct from those in vitro amyloid filaments. A very recent cryo-EM structural study also revealed that ex vivo α-synuclein filaments extracted from multiple system atrophy (MSA) patients adopt quite distinct molecular structures from those of in vitro α-synuclein filaments, suggesting the presence of co-factors for α-synuclein aggregation in vivo. Here, we report structural characterizations of α-synuclein filaments derived by a potential co-factor, tau, using cryo-EM and solid-state NMR. Our cryo-EM structure of the tau-promoted α-synuclein filament at 4.0 Å resolution is somewhat similar to one of the polymorphs of in vitro α-synuclein filaments. However, the N- and C-terminal regions of the tau-promoted α-synuclein filament have different molecular conformations. Our structural studies highlight the conformational plasticity of α-synuclein filaments, requiring additional structural investigation of not only more ex vivo α-synuclein filaments, but also in vitro α-synuclein filaments formed in the presence of diverse co-factors to better understand molecular basis of diverse molecular conformations of α-synuclein filaments.

show abstract

Automatic local resolution-based sharpening of cryo-EM maps

Cited by 21 publications

References 25 publications

Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation

Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation

Challenges and opportunities in cryo-EM single-particle analysis

Distinct cryo-EM Structure of α-synuclein Filaments derived by Tau

Contact Info

Product

Resources

About