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Yorodumi- EMDB-2762: Electron cryo-microscopy of human mitochondrial large ribosomal s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2762 | |||||||||
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Title | Electron cryo-microscopy of human mitochondrial large ribosomal subunit | |||||||||
Map data | Reconstruction of the large subunit of the human mitochondrial ribosome | |||||||||
Sample |
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Keywords | ribosome / translation | |||||||||
Function / homology | Function and homology information rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters ...rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / fibrillar center / double-stranded RNA binding / large ribosomal subunit / small ribosomal subunit rRNA binding / cell junction / large ribosomal subunit rRNA binding / 5S rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / mRNA binding / nucleotide binding / nucleolus / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Brown A / Amunts A / Bai XC / Sugimoto Y / Edwards PC / Murshudov G / Scheres SHW / Ramakrishnan V | |||||||||
Citation | Journal: Science / Year: 2014 Title: Structure of the large ribosomal subunit from human mitochondria. Authors: Alan Brown / Alexey Amunts / Xiao-Chen Bai / Yoichiro Sugimoto / Patricia C Edwards / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan / Abstract: Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial ...Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs. | |||||||||
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_2762.map.gz | 15.5 MB | EMDB map data format | |
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Header (meta data) | emd-2762-v30.xml emd-2762.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2762_fsc.xml | 11.3 KB | Display | FSC data file |
Images | EMD_2762_map_image.png | 212.5 KB | ||
Masks | emd_2762_msk_1.map | 125 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2762 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2762 | HTTPS FTP |
-Validation report
Summary document | emd_2762_validation.pdf.gz | 429 KB | Display | EMDB validaton report |
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Full document | emd_2762_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | emd_2762_validation.xml.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2762 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2762 | HTTPS FTP |
-Related structure data
Related structure data | 3j7yMC 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_2762.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the large subunit of the human mitochondrial ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Segmentation: This mask represents the large subunit of the...
Annotation | This mask represents the large subunit of the human mitochondrial ribosome | ||||||||||||
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File | emd_2762_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human mitochondrial ribosome
Entire | Name: Human mitochondrial ribosome |
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Components |
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-Supramolecule #1000: Human mitochondrial ribosome
Supramolecule | Name: Human mitochondrial ribosome / type: sample / ID: 1000 / Oligomeric state: Multimer / Number unique components: 1 |
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Molecular weight | Theoretical: 1.7 MDa |
-Supramolecule #1: Large subunit of the human mitochondrial ribosome
Supramolecule | Name: Large subunit of the human mitochondrial ribosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: 39S / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Kidney / Cell: HEK293 / Organelle: Mitochondria / Location in cell: Inner mitochondrial membrane |
Molecular weight | Theoretical: 1.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.23 mg/mL |
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Buffer | pH: 7.45 Details: 20 mM Hepes-KOH pH 7.45, 100 mM KCl, 20 mM MgOAc, 2 mM DTT |
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 | Apr 12, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1521 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |