Fitting atomic models into electron-microscopy maps
TL;DR: Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 A resolution can produce structural information that is accurate to about 2.2 A resolution, which helps to fit the component structures into the EM density maps.
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Abstract: Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 A resolution can produce structural information that is accurate to about 2.2 A resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the former of which can be off by up to 5%. It is also necessary to determine the relative height of density by using a suitable scaling function. Difference maps can identify, for instance, sites of glycosylation, the position of which helps to fit the component structures into the EM density maps. Examples are given from the analysis of alphaviruses, rhinovirus–receptor interactions and poliovirus–receptor interactions.
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Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V. Afonine,Pavel V. Afonine,Billy K. Poon,Randy J. Read,Oleg V. Sobolev,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +9 more
TL;DR: In this article, the authors describe the implementation of real-space refinement in the phenixreal_space-refine program from the PHENIX suite, which makes use of extra information such as secondary-structure and rotamer-specific restraints.
Structure of dengue virus: implications for flavivirus organization, maturation, and fusion.
Richard J. Kuhn,Wei Zhang,Michael G. Rossmann,Sergei V. Pletnev,Jeroen Corver,Edith M. Lenches,Christopher T. Jones,Suchetana Mukhopadhyay,Paul R. Chipman,Ellen G. Strauss,Timothy S. Baker,James H. Strauss +11 more
TL;DR: The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map, suggesting that flaviviruses employ a fusion mechanism in which the distal beta barrels of domain II of the glycop Protein E are inserted into the cellular membrane.
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X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
TL;DR: In this article, a review of the use of small angle X-ray scattering (SAXS) for modeling macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, is presented.
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Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
TL;DR: A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented, incorporating the EM data as an external potential added to the molecular dynamics force field.
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Outcome of the First Electron Microscopy Validation Task Force Meeting
Richard Henderson,Andrej Sali,Matthew L. Baker,Bridget Carragher,Batsal Devkota,Kenneth H. Downing,Edward H. Egelman,Zukang Feng,Joachim Frank,Joachim Frank,Nikolaus Grigorieff,Wen Jiang,Steven J. Ludtke,Ohad Medalia,Pawel A. Penczek,Peter B. Rosenthal,Michael G. Rossmann,Michael F. Schmid,Gunnar F. Schröder,Alasdair C. Steven,David L. Stokes,John D. Westbrook,Willy Wriggers,Huanwang Yang,Jasmine Young,Helen M. Berman,Wah Chiu,Gerard J. Kleywegt,Catherine L. Lawson +28 more
TL;DR: This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Validation Task Force organized by the Unified Data Resource for 3DEM and aims to increase the impact of 3DEM in biology and medicine.
556
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