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- EMDB-18539: Structure of the human 80S ribosome at 1.9 A resolution - the mol... -
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Open data
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Basic information
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Title | Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNA | |||||||||||||||
![]() | Composite map after each subtract coming from the multi-body job. | |||||||||||||||
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![]() | ribosome / cryo-electron microscopie / post-transcriptional modifications | |||||||||||||||
Function / homology | ![]() positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / axial mesoderm development / nucleolus organization / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / 90S preribosome assembly / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / GAIT complex / neural crest cell differentiation / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / laminin receptor activity / alpha-beta T cell differentiation / regulation of G1 to G0 transition / exit from mitosis / protein kinase A binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / optic nerve development / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / response to aldosterone / mammalian oogenesis stage / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / male meiosis I / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / macrophage chemotaxis / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.9 Å | |||||||||||||||
![]() | Holvec S / Barchet C / Frechin L / Hazemann I / von Loeffelholz O / Klaholz BP | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA. Authors: Samuel Holvec / Charles Barchet / Antony Lechner / Léo Fréchin / S Nimali T De Silva / Isabelle Hazemann / Philippe Wolff / Ottilie von Loeffelholz / Bruno P Klaholz / ![]() Abstract: The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo ...The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo electron microscopy structure of the 80S human ribosome resolving numerous new ribosomal RNA modifications and functionally important ions such as Zn, K and Mg, including their associated individual water molecules. The 2'-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry, resulting in a complete investigation of the >230 sites, many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerization turns out to be a key mechanism for U-A base pair stabilization in RNA in general. The structural environment of chemical modifications and ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy states and in human diseases. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 109.6 KB 109.6 KB | Display Display | ![]() |
Images | ![]() | 220.4 KB | ||
Filedesc metadata | ![]() | 21.9 KB | ||
Others | ![]() ![]() ![]() | 324 MB 475.1 MB 142.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
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Full document | ![]() | 456.1 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qoiMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Composite map after each subtract coming from the multi-body job. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Subtracted refinement of the 60S sub-unit.
File | emd_18539_additional_1.map | ||||||||||||
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Annotation | Subtracted refinement of the 60S sub-unit. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Subtracted refinement of the 40S sub-unit head.
File | emd_18539_additional_2.map | ||||||||||||
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Annotation | Subtracted refinement of the 40S sub-unit head. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Subtracted refinement of the 40S sub-unit body.
File | emd_18539_additional_3.map | ||||||||||||
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Annotation | Subtracted refinement of the 40S sub-unit body. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human 80S ribosome
+Supramolecule #1: Human 80S ribosome
+Macromolecule #1: 28S rRNA (3773-MER)
+Macromolecule #2: 5S rRNA (120-MER)
+Macromolecule #3: 5.8S rRNA (156-MER)
+Macromolecule #46: 18S rRNA (1740-MER)
+Macromolecule #4: 60S ribosomal protein L8
+Macromolecule #5: Large ribosomal subunit protein uL3
+Macromolecule #6: Large ribosomal subunit protein uL4
+Macromolecule #7: Large ribosomal subunit protein uL18
+Macromolecule #8: Large ribosomal subunit protein eL6
+Macromolecule #9: Large ribosomal subunit protein uL30
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: 60S ribosomal protein L10-like
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: 60S ribosomal protein L13a
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L18
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: 60S ribosomal protein L22
+Macromolecule #24: 60S ribosomal protein L23
+Macromolecule #25: 60S ribosomal protein L24
+Macromolecule #26: 60S ribosomal protein L23a
+Macromolecule #27: 60S ribosomal protein L26
+Macromolecule #28: 60S ribosomal protein L27
+Macromolecule #29: Large ribosomal subunit protein uL15
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L35a
+Macromolecule #35: 60S ribosomal protein L34
+Macromolecule #36: 60S ribosomal protein L35
+Macromolecule #37: 60S ribosomal protein L36
+Macromolecule #38: 60S ribosomal protein L37
+Macromolecule #39: 60S ribosomal protein L38
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L41
+Macromolecule #43: 60S ribosomal protein L36a
+Macromolecule #44: 60S ribosomal protein L37a
+Macromolecule #45: 60S ribosomal protein L28
+Macromolecule #47: 40S ribosomal protein S4, X isoform
+Macromolecule #48: 40S ribosomal protein SA
+Macromolecule #49: 40S ribosomal protein S3a
+Macromolecule #50: 40S ribosomal protein S3
+Macromolecule #51: 40S ribosomal protein S5
+Macromolecule #52: 40S ribosomal protein S7
+Macromolecule #53: 40S ribosomal protein S8
+Macromolecule #54: 40S ribosomal protein S10
+Macromolecule #55: 40S ribosomal protein S11
+Macromolecule #56: 40S ribosomal protein S15
+Macromolecule #57: 40S ribosomal protein S16
+Macromolecule #58: 40S ribosomal protein S18
+Macromolecule #59: Small ribosomal subunit protein eS19
+Macromolecule #60: 40S ribosomal protein S20
+Macromolecule #61: 40S ribosomal protein S21
+Macromolecule #62: 40S ribosomal protein S23
+Macromolecule #63: 40S ribosomal protein S26
+Macromolecule #64: 40S ribosomal protein S28
+Macromolecule #65: 40S ribosomal protein S29
+Macromolecule #66: Receptor of activated protein C kinase 1
+Macromolecule #67: 40S ribosomal protein S2
+Macromolecule #68: 40S ribosomal protein S6
+Macromolecule #69: 40S ribosomal protein S9
+Macromolecule #70: 40S ribosomal protein S12
+Macromolecule #71: 40S ribosomal protein S13
+Macromolecule #72: 40S ribosomal protein S14
+Macromolecule #73: 40S ribosomal protein S15a
+Macromolecule #74: 40S ribosomal protein S24
+Macromolecule #75: 40S ribosomal protein S25
+Macromolecule #76: 40S ribosomal protein S27
+Macromolecule #77: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #78: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #79: 40S ribosomal protein S17
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: POTASSIUM ION
+Macromolecule #82: SPERMIDINE
+Macromolecule #83: ZINC ION
+Macromolecule #84: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.6 Component:
Details: Titan Krios sample is prepared with Sodium cacodylate buffer. CryoARM 300 sample is prepared with Hepes buffer. | ||||||||||||||||||
Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | Purified from HeLa cells. |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | Image recording ID: 1 / Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6528 / Average exposure time: 3.58 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | JEOL CRYO ARM 300 |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4580 / Average exposure time: 3.0 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 38.3 |
Output model | ![]() PDB-8qoi: |