SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields

Frank, Joachim; Radermacher, Michael; Penczek, Pawel A.; Zhu, Jun; Li, Yanhong; Ladjadj, Mahieddine; Leith, A.

doi:10.1006/jsbi.1996.0030

Cited by 1,990 publications

(1,721 citation statements)

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“…It reads several file formats (CCP4 29 or MRC, BRIX or DSN6, 30 CNS 31 or XPLOR, 32 SPIDER, 33 DelPhi 34 or GRASP 35 potential maps, PRIISM, 36 NetCDF, 37,38 and DOCK 23 scoring grids), displays isosurfaces, meshes, and translucent solids, and allows interactive adjustment of thresholds, transparency, and brightness. Volume data is often displayed with related molecular models.…”

Section: Volume Viewermentioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

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Abstract:The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from

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Section: Volume Viewermentioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

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“…The crystal structure of yNap1–H2A–H2B was low‐pass filtered to 60 Å, reprojected into 372 equally spaced views, and used as the starting model for 3D classification. Because of the limited number of images and as the sample was negatively stained, only four projection matching cycles were carried out in SPIDER (Frank et al , 1996; Franzetti et al , 2002). Fitting of the crystal structure into the EM map was done with Chimera (Pettersen et al , 2004).…”

Section: Methodsmentioning

confidence: 99%

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

et al. 2016

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Nap1 is a histone chaperone involved in the nuclear import of H2A–H2B and nucleosome assembly. Here, we report the crystal structure of Nap1 bound to H2A–H2B together with in vitro and in vivo functional studies that elucidate the principles underlying Nap1‐mediated H2A–H2B chaperoning and nucleosome assembly. A Nap1 dimer provides an acidic binding surface and asymmetrically engages a single H2A–H2B heterodimer. Oligomerization of the Nap1–H2A–H2B complex results in burial of surfaces required for deposition of H2A–H2B into nucleosomes. Chromatin immunoprecipitation‐exonuclease (ChIP‐exo) analysis shows that Nap1 is required for H2A–H2B deposition across the genome. Mutants that interfere with Nap1 oligomerization exhibit severe nucleosome assembly defects showing that oligomerization is essential for the chaperone function. These findings establish the molecular basis for Nap1‐mediated H2A–H2B deposition and nucleosome assembly.

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“…From a total of 128 micrographs, the110 best ones were scanned on a Zeiss flatbed scanner, with a step size of 14 μm, corresponding to 2.76 Å on the object scale. From the originally windowed 24,826 images from the scanned micrographs, 12,678 images were manually selected and subjected to reference-free alignment and two-dimensional correspondence analysis [28] using SPIDER [29].…”

Section: Cryo-electron Microscopymentioning

confidence: 99%

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Maslov

Spremulli

Sharma

et al. 2007

Molecular and Biochemical Parasitology

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A novel type of ribonucleoprotein (RNP) complex has been described from the kinetoplastmitochondria of Leishmania tarentolae. The complex, termed the 45S SSU*, contains the 9S small subunit rRNA but does not contain the 12S large subunit rRNA. This complex is the most stable and abundant mitochondrial RNP complex present in Leishmania. As shown by tandem mass spectrometry, the complex contains at least 39 polypeptides with a combined molecular mass of almost 2.1 MDa. These components include several homologs of small subunit ribosomal proteins (S5, S6, S8 S9, S11, S15, S16, S17, S18, MRPS29); however, most of the polypeptides present are unique. Only a few of them show recognizable motifs, such as protein-protein (coiled-coil, Rhodanese) or protein-RNA (pentatricopeptide repeat) interaction domains. A cryo-electron microscopy examination of the 45S SSU* fraction reveals that 27% of particles represent SSU homodimers arranged in a head-to-tail orientation, while the majority of particles are clearly different and show an asymmetric bilobed morphology. Multiple classes of two-dimensional averages were derived for the asymmetrical particles, probably reflecting random orientations of the particles and difficulties in correlating these views with the known projections of ribosomal complexes. One class of the two-dimensional averages shows an SSU moiety attached to a protein mass or masses in a monosome-like appearance. The combined mass spectrometry and electron microscopy data thus indicate that the majority 45S SSU* particles represents a heterodimeric complex in which the SSU Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access

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SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields

Cited by 1,990 publications

References 0 publications

UCSF Chimera—A visualization system for exploratory research and analysis

UCSF Chimera—A visualization system for exploratory research and analysis

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

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