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Yorodumi- EMDB-2566: Electron cryo-microscopy of yeast mitochondrial large ribosomal s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2566 | |||||||||
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Title | Electron cryo-microscopy of yeast mitochondrial large ribosomal subunit | |||||||||
Map data | Reconstruction of yeast mitochondrial large ribosomal subunit; this map has a mask around the large ribosomal subunit | |||||||||
Sample |
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Keywords | cryo-EM / yeast mitochondrial ribosome | |||||||||
Function / homology | Function and homology information positive regulation of mitochondrial DNA replication / mitochondrial cytochrome c oxidase assembly / Mitochondrial protein degradation / mitochondrial genome maintenance / ribonuclease III activity / DNA strand exchange activity / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / cell redox homeostasis ...positive regulation of mitochondrial DNA replication / mitochondrial cytochrome c oxidase assembly / Mitochondrial protein degradation / mitochondrial genome maintenance / ribonuclease III activity / DNA strand exchange activity / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / cell redox homeostasis / large ribosomal subunit / double-stranded RNA binding / ribosome biogenesis / single-stranded DNA binding / cellular response to oxidative stress / transferase activity / large ribosomal subunit rRNA binding / DNA recombination / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / translation / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.2 Å | |||||||||
Authors | Amunts A / Brown A / Bai XC / Llacer JL / Hussain T / Emsley P / Long F / Murshudov G / Scheres SHW / Ramakrishnan V | |||||||||
Citation | Journal: Science / Year: 2014 Title: Structure of the yeast mitochondrial large ribosomal subunit. Authors: Alexey Amunts / Alan Brown / Xiao-Chen Bai / Jose L Llácer / Tanweer Hussain / Paul Emsley / Fei Long / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan / Abstract: Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single- ...Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2566.map.gz | 22.8 MB | EMDB map data format | |
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Header (meta data) | emd-2566-v30.xml emd-2566.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2566_fsc.xml | 10.5 KB | Display | FSC data file |
Images | EMD_2566.jpg | 209.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2566 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2566 | HTTPS FTP |
-Validation report
Summary document | emd_2566_validation.pdf.gz | 363.2 KB | Display | EMDB validaton report |
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Full document | emd_2566_full_validation.pdf.gz | 362.7 KB | Display | |
Data in XML | emd_2566_validation.xml.gz | 13.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2566 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2566 | HTTPS FTP |
-Related structure data
Related structure data | 3j6bMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2566.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of yeast mitochondrial large ribosomal subunit; this map has a mask around the large ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yeast Mitochondrial Large Ribosomal Subunit
Entire | Name: Yeast Mitochondrial Large Ribosomal Subunit |
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Components |
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-Supramolecule #1000: Yeast Mitochondrial Large Ribosomal Subunit
Supramolecule | Name: Yeast Mitochondrial Large Ribosomal Subunit / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 1.9 MDa / Theoretical: 1.9 MDa |
-Supramolecule #1: Yeast Mitochondrial Large Ribosomal Subunit
Supramolecule | Name: Yeast Mitochondrial Large Ribosomal Subunit / type: complex / ID: 1 / Name.synonym: 54S Mitochondrial Ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: LSU 60S |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Organelle: Mitochondrion |
Molecular weight | Experimental: 1.9 MDa / Theoretical: 1.9 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Hepes-KOH pH 7.5, 100 mM KCl, 20 mM MgOAc, 2 mM DTT |
Staining | Type: NEGATIVE / Details: cryo EM |
Grid | Details: 30 s on glow-discharged holey carbon grids (Quantifoil R2/2), onto which a home-made continuous carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK II / Method: Blot 2.5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 90 K / Average: 85 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification |
Date | May 25, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1030 / Average electron dose: 25 e/Å2 Details: An in-house built system was used to intercept the videos from the detector at a rate of 17 frames for the 1 s exposures. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |