+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4263 | |||||||||
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Title | High-resolution cryo-EM structure of the human 80S ribosome | |||||||||
Map data | Human 80S ribosomes 3D reconstruction before focused refinement (Corresponding high-resolution obtained by focused refinement is EMD-3883) | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Natchiar SK / Myasnikov AG | |||||||||
Citation | Journal: Nature / Year: 2017 Title: Visualization of chemical modifications in the human 80S ribosome structure. Authors: S Kundhavai Natchiar / Alexander G Myasnikov / Hanna Kratzat / Isabelle Hazemann / Bruno P Klaholz / Abstract: Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. ...Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA. Several of the modifications are associated with the binding sites of three ribosome-targeting antibiotics, or are associated with degenerate states in cancer, such as keto alkylations on nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way towards understanding the role of epigenetic rRNA modifications in human diseases and suggests new possibilities for designing selective inhibitors and therapeutic drugs. | |||||||||
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_4263.map.gz | 809.8 MB | EMDB map data format | |
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Header (meta data) | emd-4263-v30.xml emd-4263.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
Images | emd_4263.png | 191.3 KB | ||
Masks | emd_4263_msk_1.map | 1000 MB | Mask map | |
Others | emd_4263_half_map_1.map.gz emd_4263_half_map_2.map.gz | 809.8 MB 810.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4263 | HTTPS FTP |
-Validation report
Summary document | emd_4263_validation.pdf.gz | 435 KB | Display | EMDB validaton report |
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Full document | emd_4263_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | emd_4263_validation.xml.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4263 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4263 | HTTPS FTP |
-Related 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_4263.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human 80S ribosomes 3D reconstruction before focused refinement (Corresponding high-resolution obtained by focused refinement is EMD-3883) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4263_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Human 80S ribosomes half map before focused refinement...
File | emd_4263_half_map_1.map | ||||||||||||
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Annotation | Human 80S ribosomes half map before focused refinement (Corresponding high-resolution obtained by focused refinement is EMD-3883) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human 80S ribosomes half map before focused refinement...
File | emd_4263_half_map_2.map | ||||||||||||
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Annotation | Human 80S ribosomes half map before focused refinement (Corresponding high-resolution obtained by focused refinement is EMD-3883) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 80S ribosome with ligand HHT and HYG
Entire | Name: 80S ribosome with ligand HHT and HYG |
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Components |
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-Supramolecule #1: 80S ribosome with ligand HHT and HYG
Supramolecule | Name: 80S ribosome with ligand HHT and HYG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#81 / Details: Human 80S ribosome with modified nucleotides |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 4.3 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 / Details: 100mM KCl, 5mM MgAc2, 20mM Hepes, 10mM NH4Cl |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138234 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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