The Escherichia coli large ribosomal subunit at 7.5 Å resolution

Matadeen, Rishi; Patwardhan, Ardan; Gowen, Brent; Orlova, Elena V.; Pape, Tillmann; Cuff, M.E.; Mueller, Florian; Brimacombe, Richard; Heel, Marin van

doi:10.1016/s0969-2126(00)88348-3

Cited by 126 publications

(101 citation statements)

References 34 publications

(67 reference statements)

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“…The mismatch regions of the 50S subunit are distributed around its periphery, primarily associated with its proteins. None of the matching RNA regions participate in ligand interactions in the 30S subunit, but many of these helices in the 50S (Pioletti et al 2001;Yusupov et al 2001;Klaholz et al 2003;Rawat et al 2003) and regions found to be flexible in comparative structural studies (see Matadeen et al 1999;Yusupov et al 2001;Ogle et al 2002;Klaholz et al 2003;Rawat et al 2003) mapped into crystal structures of the 30S subunit (PDB identification: 1GIX; Yusupov et al 2001). (D) Secondary structure diagram of the 23S RNA, 5S RNA, and associated proteins, colored in dark gold if data available for the region generally were in good agreement (<25% of mismatch); blue, >25% of mismatches; and gray, no data in our data set.…”

Section: Distribution Of Mismatchesmentioning

confidence: 99%

“…The same color scheme as in D, but rendered in three dimensions. (F) Ligand-binding regions and regions found to be flexible in comparative structural studies (Matadeen et al 1999;Yusupov et al 2001;Klaholz et al 2003;Rawat et al 2003) mapped into crystal structures of the 50S subunit (PDB identification: 1GIY; Yusupov et al 2001). Landmarks show macroscopic features of the 30S and 50S subunits known from electron microscopy: h indicates head; bk, beak; sp, spur; and CP, central protuberance (where the 5S RNA is located); as well as proteins L1, L9, and L7/L12 dimer.…”

Section: Distribution Of Mismatchesmentioning

confidence: 99%

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Ribosomal dynamics inferred from variations in experimental measurements

Gabashvili

Whirl‐Carrillo²,

Bada³

et al. 2003

RNA

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The crystal structures of the ribosome reveal remarkable complexity and provide a starting set of snapshots with which to understand the dynamics of translation. To augment the static crystallographic models with dynamic information present in crosslink, footprint, and cleavage data, we examined 2691 proximity measurements and focused on the subset that was apparently incompatible with >40 published crystal structures. The measurements from this subset generally involve regions of the structure that are functionally conserved and structurally flexible. Local movements in the crystallographic states of the ribosome that would satisfy biochemical proximity measurements show coherent patterns suggesting alternative conformations of the ribosome. Three different types of data obtained for the two subunits display similar "mismatching" patterns, suggesting that the signals are robust and real. In particular, there is an indication of coherent motion in the decoding region within the 30S subunit and central protuberance and surrounding areas of the 50S subunit. Directions of rearrangements fluctuate around the proposed path of tRNA translocation and the plane parallel to the interface of the two subunits. Our results demonstrate that systematic combination and analysis of noisy, apparently incompatible data sources can provide biologically useful signals about structural dynamics.

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Section: Distribution Of Mismatchesmentioning

confidence: 99%

Section: Distribution Of Mismatchesmentioning

confidence: 99%

Ribosomal dynamics inferred from variations in experimental measurements

Gabashvili

Whirl‐Carrillo²,

Bada³

et al. 2003

RNA

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“…Failure to correct the CTF accurately can produce significant mass misplacements in the 3-D reconstruction, such as the exaggeration of holes and protrusions. Various methods for making CTF corrections during the 3-D reconstruction of single particles have been introduced (for instance, Böt-tcher et al, 1997;Trus et al, 1997;Zhu et al, 1997;Conway and Steven, 1999;Ludtke et al, 1999;Matadeen et al, 1999;Zhou et al, 2000). Improper correction of E(s) will lead to either a model in which real features are not resolvable or one in which noisy features are unduly magnified.…”

Section: Theoretical Backgroundmentioning

confidence: 99%

“…Because of advances in experimental and computational techniques, the resolution of single particle reconstructions has reached beyond 9 Å (Böttcher et al, 1997;Conway et al, 1997;Trus et al, 1997;Matadeen et al, 1999;Mancini et al, 2000;Zhou et al, 2000). In order to extend the analysis toward atomic resolution, it will be necessary to include many more particle images containing high-resolution information (Henderson, 1995;Glaeser, 1999;Thuman-Commike et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

Fourier Amplitude Decay of Electron Cryomicroscopic Images of Single Particles and Effects on Structure Determination

Saâd

Ludtke

Jakana

et al. 2001

Journal of Structural Biology

102

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Several factors, including spatial and temporal coherence of the electron microscope, specimen movement, recording medium, and scanner optics, contribute to the decay of the measured Fourier amplitude in electron image intensities. We approximate the combination of these factors as a single Gaussian envelope function, the width of which is described by a single experimental B-factor. We present an improved method for estimating this Bfactor from individual micrographs by combining the use of X-ray solution scattering and numerical fitting to the average power spectrum of particle images. A statistical estimation from over 200 micrographs of herpes simplex virus type-1 capsids was used to estimate the spread in the experimental B-factor of the data set. The B-factor is experimentally shown to be dependent on the objective lens defocus setting of the microscope. The average Bfactor, the X-ray scattering intensity of the specimen, and the number of particles required to determine the structure at a lower resolution can be used to estimate the minimum fold increase in the number of particles that would be required to extend a single particle reconstruction to a specified higher resolution. We conclude that microscope and imaging improvements to reduce the experimental Bfactor will be critical for obtaining an atomic resolution structure.

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“…Examples include studies of various viruses Böttcher et al, 1997b;Conway et al, 1997;Leiman et al, 2004;Morais et al, 2005;Zhou et al, 2000), virus/receptor complexes (Belnap et al, 2000;Bubeck et al, 2005;Hewat et al, 2000;Rossmann et al, 2002;Xiao et al, 2005a), many important cellular complexes such as ribosomes (Allen et al, 2005;Matadeen et al, 1999), nuclear pores (Beck et al, 2004), bacterial flagella (Yonekura et al, 2005), GroEL , membrane Ca 2+ channels (Serysheva et al, 2005), ATPases (Bernal and Stock, 2004;Chen et al, 2004), and many large protein complexes (Acehan et al, 2002;Cheng et al, 2004;Ishikawa et al, 2004;Zhou et al, 2001). Cryo-EM has significantly improved in the last ten years to achieve sub-nanometer resolution, where secondary structural features become visible (Böttcher et al, 1997b;Conway et al, 1997;van Heel et al, 2000;Zhou et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Interpretation of electron density with stereographic roadmap projections

Xiao

Rossmann

2007

Journal of Structural Biology

138

116

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The program RIVEM (Radial Interpretation of Viral Electron density Maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. This permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. The features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. The procedure can also be adapted for the investigation of various molecular interactions.

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The Escherichia coli large ribosomal subunit at 7.5 Å resolution

Cited by 126 publications

References 34 publications

Ribosomal dynamics inferred from variations in experimental measurements

Ribosomal dynamics inferred from variations in experimental measurements

Fourier Amplitude Decay of Electron Cryomicroscopic Images of Single Particles and Effects on Structure Determination

Interpretation of electron density with stereographic roadmap projections

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