EMDB-6044: Ribosome conformation along minimum free-energy trajectory

Basic information

• Entry: Database: EMDB / ID: EMD-6044
• Title: Ribosome conformation along minimum free-energy trajectory
• Map data: Conformation of yeast ribosome

Sample

• Sample: Yeast 80S ribosomeEukaryotic ribosome
• Complex: 80S ribosomeEukaryotic ribosome

• Keywords: Translocation / energy landscape / conformations / Brownian machine
• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 20.0 Å
• Authors: Dashti A / Schwander P / Langlois R / Fung R / Li W / Hosseinizadeh A / Liao HY / Pallesen J / Sharma G / Stupina VA / Simon AE / Dinman J / Frank J / Ourmazd A
• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2014; Title: Trajectories of the ribosome as a Brownian nanomachine.; Authors: Ali Dashti / Peter Schwander / Robert Langlois / Russell Fung / Wen Li / Ahmad Hosseinizadeh / Hstau Y Liao / Jesper Pallesen / Gyanesh Sharma / Vera A Stupina / Anne E Simon / Jonathan D Dinman / Joachim Frank / Abbas Ourmazd / ; Abstract: A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.

History

Deposition	Aug 22, 2014	-
Header (metadata) release	Oct 8, 2014	-
Map release	Oct 8, 2014	-
Update	May 27, 2015	-
Current status	May 27, 2015	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_6044.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Conformation of yeast ribosome
• Voxel size: X=Y=Z: 3 Å

Density

Contour Level	By EMDB: 17.0 / Movie #1: 17
Minimum - Maximum	-59.835098270000003 - 113.681358340000003
Average (Standard dev.)	5.43819237 (±11.54793358)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 125 125 125 Spacing 125 125 125
Cell	A=B=C: 375.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	3	3	3
M x/y/z	125	125	125
origin x/y/z	0.000	0.000	0.000
length x/y/z	375.000	375.000	375.000
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	125	125	125
D min/max/mean	-59.835	113.681	5.438

Supplemental data

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Sample components

Entire : Yeast 80S ribosome

• Entire: Name: Yeast 80S ribosomeEukaryotic ribosome

Components

• Sample: Yeast 80S ribosomeEukaryotic ribosome
• Complex: 80S ribosomeEukaryotic ribosome

Supramolecule #1000: Yeast 80S ribosome

• Supramolecule: Name: Yeast 80S ribosome / type: sample / ID: 1000 / Number unique components: 1

Supramolecule #1: 80S ribosome

• Supramolecule: Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Grid: Details: carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH, Jena, Germany)
• Vitrification: Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

Electron microscopy

• Microscope: FEI POLARA 300
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal magnification: 80000
• Sample stage: Specimen holder model: GATAN LIQUID NITROGEN
• Date: Jan 1, 2010
• Image recording: Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Ų
• Experimental equipment: Model: Tecnai Polara / Image courtesy: FEI Company

Image processing

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Number images used: 849914