+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10690 | ||||||||||||
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Title | Cryo-EM map of human ribosome in hybrid-PRE state | ||||||||||||
Map data | Cryo-EM map of human ribosome in the hybrid-PRE state | ||||||||||||
Sample |
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Keywords | hybrid-PRE state / RIBOSOME | ||||||||||||
Function / homology | Function and homology information eukaryotic 80S initiation complex / : / negative regulation of protein neddylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / ribosomal protein import into nucleus ...eukaryotic 80S initiation complex / : / negative regulation of protein neddylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / ribosomal protein import into nucleus / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / TORC2 complex binding / negative regulation of RNA splicing / negative regulation of DNA repair / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / NF-kappaB complex / middle ear morphogenesis / neural crest cell differentiation / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / A band / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / 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 / pigmentation / protein kinase A binding / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / optic nerve development / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / retinal ganglion cell axon guidance / mammalian oogenesis stage / homeostatic process / positive regulation of mitochondrial depolarization / G1 to G0 transition / activation-induced cell death of T cells / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / lung morphogenesis / iron-sulfur cluster binding / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / male meiosis I / positive regulation of activated T cell proliferation / monocyte chemotaxis / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / regulation of cell division / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Bhaskar V / Schenk AD | ||||||||||||
Funding support | Switzerland, France, 3 items
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Citation | Journal: Cell Rep / Year: 2020 Title: Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes. Authors: Varun Bhaskar / Alexandra Graff-Meyer / Andreas D Schenk / Simone Cavadini / Ottilie von Loeffelholz / S Kundhavai Natchiar / Caroline G Artus-Revel / Hans-Rudolf Hotz / Gabriel Bretones / ...Authors: Varun Bhaskar / Alexandra Graff-Meyer / Andreas D Schenk / Simone Cavadini / Ottilie von Loeffelholz / S Kundhavai Natchiar / Caroline G Artus-Revel / Hans-Rudolf Hotz / Gabriel Bretones / Bruno P Klaholz / Jeffrey A Chao / Abstract: Ribosomes undergo multiple conformational transitions during translation elongation. Here, we report the high-resolution cryoelectron microscopy (cryo-EM) structure of the human 80S ribosome in the ...Ribosomes undergo multiple conformational transitions during translation elongation. Here, we report the high-resolution cryoelectron microscopy (cryo-EM) structure of the human 80S ribosome in the post-decoding pre-translocation state (classical-PRE) at 3.3-Å resolution along with the rotated (hybrid-PRE) and the post-translocation states (POST). The classical-PRE state ribosome structure reveals a previously unobserved interaction between the C-terminal region of the conserved ribosomal protein uS19 and the A- and P-site tRNAs and the mRNA in the decoding site. In addition to changes in the inter-subunit bridges, analysis of different ribosomal conformations reveals the dynamic nature of this domain and suggests a role in tRNA accommodation and translocation during elongation. Furthermore, we show that disease-associated mutations in uS19 result in increased frameshifting. Together, this structure-function analysis provides mechanistic insights into the role of the uS19 C-terminal tail in the context of mammalian ribosomes. | ||||||||||||
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_10690.map.gz | 67 MB | EMDB map data format | |
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Header (meta data) | emd-10690-v30.xml emd-10690.xml | 101.4 KB 101.4 KB | Display Display | EMDB header |
Images | emd_10690.png | 64.3 KB | ||
Filedesc metadata | emd-10690.cif.gz | 19.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10690 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10690 | HTTPS FTP |
-Validation report
Summary document | emd_10690_validation.pdf.gz | 260.2 KB | Display | EMDB validaton report |
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Full document | emd_10690_full_validation.pdf.gz | 259.4 KB | Display | |
Data in XML | emd_10690_validation.xml.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10690 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10690 | HTTPS FTP |
-Related structure data
Related structure data | 6y57MC 6y0gC 6y2lC C: citing same article (ref.) M: atomic model generated by this map |
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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_10690.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of human ribosome in the hybrid-PRE state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 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 : Human ribosomes in the classical-PRE state
+Supramolecule #1: Human ribosomes in the classical-PRE state
+Macromolecule #1: mRNA
+Macromolecule #2: P/E tRNA
+Macromolecule #3: A/P tRNA
+Macromolecule #4: 28S ribosomal RNA
+Macromolecule #5: 5S ribosomal RNA
+Macromolecule #6: 5.8S ribosomal RNA
+Macromolecule #49: 18S ribosomal RNA
+Macromolecule #7: 60S ribosomal protein L8
+Macromolecule #8: 60S ribosomal protein L3
+Macromolecule #9: 60S ribosomal protein L4
+Macromolecule #10: 60S ribosomal protein L5
+Macromolecule #11: 60S ribosomal protein L6
+Macromolecule #12: 60S ribosomal protein L7
+Macromolecule #13: 60S ribosomal protein L7a
+Macromolecule #14: 60S ribosomal protein L9
+Macromolecule #15: 60S ribosomal protein L10-like
+Macromolecule #16: 60S ribosomal protein L11
+Macromolecule #17: 60S ribosomal protein L13
+Macromolecule #18: 60S ribosomal protein L14
+Macromolecule #19: 60S ribosomal protein L15
+Macromolecule #20: 60S ribosomal protein L13a
+Macromolecule #21: 60S ribosomal protein L17
+Macromolecule #22: 60S ribosomal protein L18
+Macromolecule #23: 60S ribosomal protein L19
+Macromolecule #24: 60S ribosomal protein L18a
+Macromolecule #25: 60S ribosomal protein L21
+Macromolecule #26: 60S ribosomal protein L22
+Macromolecule #27: 60S ribosomal protein L23
+Macromolecule #28: 60S ribosomal protein L24
+Macromolecule #29: 60S ribosomal protein L23a
+Macromolecule #30: 60S ribosomal protein L26
+Macromolecule #31: 60S ribosomal protein L27
+Macromolecule #32: 60S ribosomal protein L27a
+Macromolecule #33: 60S ribosomal protein L29
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L35a
+Macromolecule #38: 60S ribosomal protein L34
+Macromolecule #39: 60S ribosomal protein L35
+Macromolecule #40: 60S ribosomal protein L36
+Macromolecule #41: 60S ribosomal protein L37
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: Ubiquitin-60S ribosomal protein L40
+Macromolecule #45: 60S ribosomal protein L41
+Macromolecule #46: 60S ribosomal protein L36a
+Macromolecule #47: 60S ribosomal protein L37a
+Macromolecule #48: 60S ribosomal protein L28
+Macromolecule #50: 40S ribosomal protein SA
+Macromolecule #51: 40S ribosomal protein S3a
+Macromolecule #52: 40S ribosomal protein S2
+Macromolecule #53: 40S ribosomal protein S3
+Macromolecule #54: 40S ribosomal protein S4, X isoform
+Macromolecule #55: 40S ribosomal protein S5
+Macromolecule #56: 40S ribosomal protein S6
+Macromolecule #57: 40S ribosomal protein S7
+Macromolecule #58: 40S ribosomal protein S8
+Macromolecule #59: 40S ribosomal protein S9
+Macromolecule #60: 40S ribosomal protein S10
+Macromolecule #61: 40S ribosomal protein S11
+Macromolecule #62: 40S ribosomal protein S13
+Macromolecule #63: 40S ribosomal protein S14
+Macromolecule #64: 40S ribosomal protein S15
+Macromolecule #65: 40S ribosomal protein S16
+Macromolecule #66: 40S ribosomal protein S17
+Macromolecule #67: 40S ribosomal protein S18
+Macromolecule #68: 40S ribosomal protein S19
+Macromolecule #69: 40S ribosomal protein S20
+Macromolecule #70: 40S ribosomal protein S21
+Macromolecule #71: 40S ribosomal protein S15a
+Macromolecule #72: 40S ribosomal protein S23
+Macromolecule #73: 40S ribosomal protein S24
+Macromolecule #74: 40S ribosomal protein S25
+Macromolecule #75: 40S ribosomal protein S26
+Macromolecule #76: 40S ribosomal protein S27
+Macromolecule #77: 40S ribosomal protein S28
+Macromolecule #78: 40S ribosomal protein S29
+Macromolecule #79: 40S ribosomal protein S30
+Macromolecule #80: 40S ribosomal protein S12
+Macromolecule #81: Receptor of activated protein C kinase 1
+Macromolecule #82: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: ZINC ION
+Macromolecule #85: water
-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: 7.6 Component:
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Grid | Model: Quantifoil R2/2 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: OTHER | ||||||||||
Output model | PDB-6y57: |