Three-dimensional structure of 50 S Escherichia coli ribosomal subunits depleted of proteins L7/L12

Carazo, José Marı́a; Wagenknecht, Terence; Radermacher, Michael; Mandiyan, Valsan; Boublík, M.; Frank, Joachim

doi:10.1016/0022-2836(88)90146-5

Cited by 23 publications

(12 citation statements)

References 27 publications

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“…This destabilization often results in a sample that exhibits a variety of shapes, some closely resembling the intact molecule, and some showing varying degrees of rearrangements. Large scale conformational changes, for example, were observed during the study of the structure of the 50S ribosomal subunit from Escherichia coli when subunits or the 5S rRNA were removed (Carazo et al, 1988) (Radermacher et al, 1990). In the current study, we observed a similar effect in a subset of the data.…”

Section: Discussionmentioning

confidence: 97%

Direct localization of the 51 and 24 kDa subunits of mitochondrial complex I by three-dimensional difference imaging

Clason

Zickermann

Ruíz

et al. 2007

Journal of Structural Biology

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Complex I is the largest complex in the respiratory chain, and the least understood. We have determined the 3D structure of complex I from Yarrowia lipolytica lacking the flavoprotein part of the N-module, which consists of the 51 kDa (NUBM) and the 24 kDa (NUHM) subunits. The reconstruction was determined by 3D electron microscopy of single particles. A comparison to our earlier reconstruction of the complete Y. lipolytica complex I clearly assigns the two flavoprotein subunits to an outer lobe of the peripheral arm of complex I. Localizing the two subunits allowed us to fit the X-ray structure of the hydrophilic fragment of complex I from Thermus thermophilus. The fit that is most consistent with previous immuno-electron microscopic data predicts that the ubiquinone reducing catalytic center resides in the second peripheral lobe, while the 75 kDa subunit is placed near the previously seen connection between the peripheral arm and the membrane arm protrusions.

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Section: Discussionmentioning

confidence: 97%

Direct localization of the 51 and 24 kDa subunits of mitochondrial complex I by three-dimensional difference imaging

Clason

Zickermann

Ruíz

et al. 2007

Journal of Structural Biology

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“…A specimen field containing particles in the preferred orientation was imaged with the specimen tilted to 45°and with the specimen in the untilted position. Particle projections appearing in the tilted image form a random conical projection set, since the particles assume random orientations with respect to an axis perpendicular to the specimen plane (27,(35)(36)(37). One of the major advantages of this method is that only one exposure of the specimen area is necessary, thus minimizing radiation damage to the molecule.…”

Section: Fig 2 Electron Micrographs Of Negatively Stained Preparatimentioning

confidence: 99%

Structure of the Multidrug Resistance P-glycoprotein to 2.5 nm Resolution Determined by Electron Microscopy and Image Analysis

Rosenberg

Callaghan

Ford

et al. 1997

Journal of Biological Chemistry

324

241

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P-glycoprotein (P-gp) is a member of the ATP binding cassette superfamily of active transporters and can confer multidrug resistance on cells and tumors by pumping chemotherapeutic drugs from the cytoplasm. P-gp was purified from CHrB30 cells and retained the ability to bind substrates and hydrolyze ATP. Labeling of P-gp with lectin-gold particles suggested it is monomeric. An initial structure of purified P-gp was determined to 2.5 nm resolution by electron microscopy and single particle image analysis of both detergent-solubilized and lipid-reconstituted protein. The structure was further refined by three dimensional reconstructions from single particle images and by Fourier projection maps of small two-dimensional crystalline arrays (unit cell parameters: a, 14.2 nm; b, 18.5 nm; and gamma, 91.6 degrees ). When viewed from above the membrane plane the protein is toroidal, with 6-fold symmetry and a diameter of about 10 nm. There is a large central pore of about 5 nm in diameter, which is closed at the inner (cytoplasmic) face of the membrane, forming an aqueous chamber within the membrane. An opening from this chamber to the lipid phase is present. The projection of the protein perpendicular to the membrane is roughly rectangular with a maximum depth of 8 nm and two 3-nm lobes exposed at the cytoplasmic face of the membrane, likely to correspond to the nucleotide binding domains. This study provides the first experimental insight into the three-dimensional architecture of any ATP binding cassette transporter.

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“…After this, the original, unaveraged images are aligned relative to the 5" averages. This procedure has been successfully applied in the reconstruction of the 'Note added in proof: The described method has been tested and proved to be sufficiently accurate (e.g., within 1/3 of a resolution element of the final reconstruction, Carazo et al, 1988). It is now the method primarily used.…”

Section: Alignment Of the Tilted Particle Imagesmentioning

confidence: 99%

Three‐Dimensional reconstruction of single particles from random and nonrandom tilt series

Radermacher

1988

J. Elec. Microsc. Tech.

484

337

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To overcome the radiation damage-induced limitations to the resolution of three-dimensional reconstructions from electron microscopic tilt series, novel reconstruction schemes have been developed that require only a single exposure of the specimen. The tilt series collected with these methods have random projection directions. First, three-dimensional reconstruction techniques are described that are applicable to data obtained from tilt series with regular tilt geometry, followed by the extensions of these techniques to permit analysis of projection series with randomly spaced tilts. The main emphasis is placed on the weighted back-projection methods, which have recently been extended so as to be applicable to random tilt series. Besides a description of the algorithms, the complete procedure for a three-dimensional reconstruction from a single-exposure, random conical tilt series is explained, including the determination of the azimuthal angles, the alignment scheme for conical tilt series, the dependence of the achievable resolution on the number of projections for regular conical and single-axis geometries, and the method to calculate the actual resolution of two-dimensional image averages and of three-dimensional reconstructions using the phase residual and Fourier ring correlation criteria. Examples are given of biological specimens to which these three-dimensional reconstruction methods have been applied.

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Three-dimensional structure of 50 S Escherichia coli ribosomal subunits depleted of proteins L7/L12

Cited by 23 publications

References 27 publications

Direct localization of the 51 and 24 kDa subunits of mitochondrial complex I by three-dimensional difference imaging

Direct localization of the 51 and 24 kDa subunits of mitochondrial complex I by three-dimensional difference imaging

Structure of the Multidrug Resistance P-glycoprotein to 2.5 nm Resolution Determined by Electron Microscopy and Image Analysis

Three‐Dimensional reconstruction of single particles from random and nonrandom tilt series

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