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	Overcoming resolution attenuation during tilted cryo-EM data collection.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 389, Year 2024
Publish date	Jan 9, 2024
Authors	Sriram Aiyer / Philip R Baldwin / Shi Min Tan / Zelin Shan / Juntaek Oh / Atousa Mehrani / Marianne E Bowman / Gordon Louie / Dario Oliveira Passos / Selena Đorđević-Marquardt / Mario Mietzsch / Joshua A Hull / Shuichi Hoshika / Benjamin A Barad / Danielle A Grotjahn / Robert McKenna / Mavis Agbandje-McKenna / Steven A Benner / Joseph A P Noel / Dong Wang / Yong Zi Tan / Dmitry Lyumkis /
PubMed Abstract	Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding ...Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
External links	Nat Commun / PubMed:38195598 / PubMed Central
Methods	EM (single particle)
Resolution	1.92 - 3.2 Å
Structure data	EMDB-36766: Untilted (0 Degree Tilted) Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.1 Å EMDB-36767: 10 Degree Tilted Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.1 Å EMDB-36768: 20 Degree Tilted Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.1 Å EMDB-36769: 30 Degree Tilted Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.1 Å EMDB-36770: 40 Degree Tilted Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.1 Å EMDB-36771: 50 Degree Tilted Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.1 Å EMDB-36772: 60 Degree Tilted Single-Particle CryoEM Reconstruction of AAV2 Viral Capsid Method: EM (single particle) / Resolution: 2.2 Å EMDB-36807: Untilted (0 Degree Tilted) Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.2 Å EMDB-36809: 10 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.3 Å EMDB-36810: 20 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.3 Å EMDB-36811: 30 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.2 Å EMDB-36812: 40 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.4 Å EMDB-36813: 60 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.5 Å EMDB-36814: 50 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 2.3 Å EMDB-36816: Untilted (0 Degree Tilted) Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 2.6 Å EMDB-36817: 10 Degree Tilted Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 2.8 Å EMDB-36818: 20 Degree Tilted Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 2.7 Å EMDB-36819: 30 Degree Tilted Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 3.0 Å EMDB-36820: 40 Degree Tilted Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 3.2 Å EMDB-36821: 50 Degree Tilted Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 2.9 Å EMDB-36822: 60 Degree Tilted Single-Particle CryoEM Reconstruction of DPS Method: EM (single particle) / Resolution: 3.2 Å EMDB-41230: Untilted (0 Degree Tilted) Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 1.92 Å EMDB-41231: 30 Degree Tilted Single-Particle CryoEM Reconstruction of Apoferritin Method: EM (single particle) / Resolution: 1.99 Å 41695 8txo EMDB-41695: 60 Degree Tilted Single-Particle CryoEM Reconstruction of RNA polymerase PDB-8txo: E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dZ-PTP base pair in the active site Method: EM (single particle) / Resolution: 3.1 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-S9F: [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Source	Homo sapiens (human) escherichia coli (E. coli) synthetic construct (others)
Keywords	TRANSCRIPTION / complex / unnatural base pairs / synthetic biology