scholarly journals Organization of transmembrane helices in photosystem II: comparison of plants and cyanobacteria

2002 ◽  
Vol 357 (1426) ◽  
pp. 1329-1335 ◽  
Author(s):  
J. Barber ◽  
J. Nield
Keyword(s):  
Electron Microscopy ◽  
Photosystem Ii ◽  
3D Structure ◽  
Structural Data ◽  
Reaction Centre ◽  
Transmembrane Helices ◽  
Light Harvesting Complex ◽  
X Ray ◽  
X Ray Crystallography ◽  
Light Harvesting Complex Ii

Electron microscopy and X–ray crystallography are revealing the structure of photosystem II. Electron crystallography has yielded a 3D structure at sufficient resolution to identify subunit positioning and transmembrane organization of the reaction–centre core complex of spinach. Single–particle analyses are providing 3D structures of photosystem II–light–harvesting complex II supercomplexes that can be used to incorporate high–resolution structural data emerging from electron and X–ray crystallography. The positions of the chlorins and metal centres within photosystem II are now available. It can be concluded that photosystem II is a dimeric complex with the transmembrane helices of CP47/D2 proteins related to those of the CP43/D1 proteins by a twofold axis within each monomer. Further, both electron microscopy and X–ray analyses show that P 680 is not a 'special pair‘ and that cytochrome b 559 is located on the D2 side of the reaction centres some distance from P 680 . However, although comparison of the electron microscopy and X–ray models for spinach and Synechococcus elongatus show considerable similarities, there seem to be differences in the number and positioning of some small subunits.

Photosystem II: the engine of life

2003 ◽  
Vol 36 (1) ◽  
pp. 71-89 ◽  
Author(s):  
James Barber
Keyword(s):  
High Resolution ◽  
Photosystem Ii ◽  
Water Oxidation ◽  
Structural Models ◽  
Reaction Centre ◽  
Ps Ii ◽  
X Ray ◽  
X Ray Crystallography ◽  
Redox Active ◽  
Resolution Electron

1. Introduction 712. Electron transfer in PS II 723. (Mn)4cluster and mechanism of water oxidation 734. Organization and structure of the protein subunits 755. Organization of chlorophylls and redox active cofactors 816. Implications arising from the structural models 827. Perspectives 848. Acknowledgements 869. Addendum 8610. References 87Photosystem II (PS II) is a multisubunit membrane protein complex, which uses light energy to oxidize water and reduce plastoquinone. High-resolution electron cryomicroscopy and X-ray crystallography are revealing the structure of this important molecular machine. Both approaches have contributed to our understanding of the organization of the transmembrane helices of higher plant and cyanobacterial PS II and both indicate that PS II normally functions as a dimer. However the high-resolution electron density maps derived from X-ray crystallography currently at 3·7/3·8 Å, have allowed assignments to be made to the redox active cofactors involved in the light-driven water–plastoquinone oxidoreductase activity and to the chlorophyll molecules that absorb and transfer energy to the reaction centre. In particular the X-ray work has identified density that can accommodate the four manganese atoms which catalyse the water-oxidation process. The Mn cluster is located at the lumenal surface of the D1 protein and approximately 7 Å from the redox active tyrosine residue (YZ) which acts an electron/proton transfer link to the primary oxidant P680.+. The lower resolution electron microscopy studies, however, are providing structural models of larger PS II supercomplexes that are ideal frameworks in which to incorporate the X-ray derived structures.

scholarly journals qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

2020 ◽  
Author(s):  
Blake T. Riley ◽  
Stephanie A. Wankowicz ◽  
Saulo H. P. de Oliveira ◽  
Gydo C. P. van Zundert ◽  
Daniel Hogan ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Structural Data ◽  
Conformational Ensemble ◽  
Distributed Application ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Formidable Challenge ◽  
Density Maps

AbstractNew X-ray crystallography and cryo-electron microscopy (cryo-EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open-source under the MIT license, and is available at https://github.com/ExcitedStates/qfit-3.0.

Electron microscopy of rabbit FC crystals

1983 ◽  
Vol 41 ◽  
pp. 730-731
Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Resolution Electron Microscopy ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Replacement Technique ◽  
Hydrated Crystal ◽  
Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

scholarly journals High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Koji Kato ◽  
Naoyuki Miyazaki ◽  
Tasuku Hamaguchi ◽  
Yoshiki Nakajima ◽  
Fusamichi Akita ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Physiological State ◽  
High Dose ◽  
Final State ◽  
X Ray ◽  
Redox States ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Redox Active ◽  
Beam Damage

AbstractPhotosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

scholarly journals Synthesis of Three-Dimensional Fe3O4/Graphene Aerogels for the Removal of Arsenic Ions from Water

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Yan Ye ◽  
Da Yin ◽  
Bin Wang ◽  
Qingwen Zhang
Keyword(s):  
Electron Microscopy ◽  
Photoelectron Spectroscopy ◽  
3D Structure ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Graphene Aerogels ◽  
Transmission Electron ◽  
Potential Applications ◽  
Removal Of Arsenic

We report the synthesis of three-dimensional Fe3O4/graphene aerogels (GAs) and their application for the removal of arsenic (As) ions from water. The morphology and properties of Fe3O4/GAs have been characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and superconducting quantum inference device. The 3D nanostructure shows that iron oxide nanoparticles are decorated on graphene with an interconnected network structure. It is found that Fe3O4/GAs own a capacity of As(V) ions adsorption up to 40.048 mg/g due to their remarkable 3D structure and existence of magnetic Fe3O4nanoparticles for separation. The adsorption isotherm matches well with the Langmuir model and kinetic analysis suggests that the adsorption process is pseudo-second-ordered. In addition to the excellent adsorption capability, Fe3O4/GAs can be easily and effectively separated from water, indicating potential applications in water treatment.

scholarly journals Structure of the Lassa Virus Nucleoprotein Revealed by X-ray Crystallography, Small-angle X-ray Scattering, and Electron Microscopy

2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Lassa Virus ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Ray Scattering
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