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Yorodumi- EMDB-12535: Structure of the yeast Gcn1 bound to a colliding stalled 80S ribo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12535 | |||||||||
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Title | Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA | |||||||||
Map data | map colliding ribosome | |||||||||
Sample |
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Function / homology | Function and homology information maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / transcription coactivator activity / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.36 Å | |||||||||
Authors | Pochopien AA / Beckert B / Wilson DN | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Authors: Agnieszka A Pochopien / Bertrand Beckert / Sergo Kasvandik / Otto Berninghausen / Roland Beckmann / Tanel Tenson / Daniel N Wilson / Abstract: The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for ...The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for the kinase Gcn2, which in turn is activated by stalled ribosomes, leading to phosphorylation of eIF2 and a subsequent global repression of translation. The fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, a negative regulator of Gcn2. Despite the wealth of available biochemical data, information on structures of Gcn proteins on the ribosome has remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the P-stalk and the A-site region of the lead ribosome. The lead ribosome is stalled in a nonrotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, and Rbg2/Gir2 in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site, and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings reveal the interaction mode of the Gcn2-activating protein Gcn1 with colliding ribosomes and provide insight into the regulation of Gcn2 activation. The binding of Gcn1 to a disome has important implications not only for the Gcn2-activated ISR, but also for the general ribosome-associated quality control pathways. | |||||||||
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_12535.map.gz | 697.8 MB | EMDB map data format | |
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Header (meta data) | emd-12535-v30.xml emd-12535.xml | 97.9 KB 97.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12535_fsc.xml | 25 KB | Display | FSC data file |
Images | emd_12535.png | 174.2 KB | ||
Others | emd_12535_additional_1.map.gz emd_12535_additional_2.map.gz emd_12535_additional_3.map.gz emd_12535_half_map_1.map.gz emd_12535_half_map_2.map.gz | 251.2 MB 11.5 MB 48.9 MB 1 GB 1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12535 | HTTPS FTP |
-Validation report
Summary document | emd_12535_validation.pdf.gz | 367.7 KB | Display | EMDB validaton report |
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Full document | emd_12535_full_validation.pdf.gz | 366.8 KB | Display | |
Data in XML | emd_12535_validation.xml.gz | 29.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12535 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12535 | HTTPS FTP |
-Related structure data
Related structure data | 7nrdMC 7nrcC 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_12535.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map colliding ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: map colliding ribosome relion final run
File | emd_12535_additional_1.map | ||||||||||||
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Annotation | map colliding ribosome relion final run | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focus refinement 40S only and postprocess
File | emd_12535_additional_2.map | ||||||||||||
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Annotation | focus refinement 40S only and postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: map colliding ribosome postprocess
File | emd_12535_additional_3.map | ||||||||||||
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Annotation | map colliding ribosome postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map colliding ribosome
File | emd_12535_half_map_1.map | ||||||||||||
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Annotation | Half map colliding ribosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map colliding ribosome
File | emd_12535_half_map_2.map | ||||||||||||
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Annotation | Half map colliding ribosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of the yeast Gcn1-bound coilliding stalled 80S ribosome...
+Supramolecule #1: Structure of the yeast Gcn1-bound coilliding stalled 80S ribosome...
+Macromolecule #1: TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete ...
+Macromolecule #36: mRNA (32-MER)
+Macromolecule #37: tRNA (75-MER)
+Macromolecule #38: tRNA (77-MER)
+Macromolecule #39: 25S rRNA (3184-MER)
+Macromolecule #40: 5S rRNA (121-MER)
+Macromolecule #41: 5.8S rRNA (158-MER)
+Macromolecule #2: 40S ribosomal protein S3
+Macromolecule #3: 40S ribosomal protein S5
+Macromolecule #4: 40S ribosomal protein S10-A
+Macromolecule #5: 40S ribosomal protein S12
+Macromolecule #6: 40S ribosomal protein S15
+Macromolecule #7: 40S ribosomal protein S16-A
+Macromolecule #8: 40S ribosomal protein S17-B
+Macromolecule #9: 40S ribosomal protein S18-A
+Macromolecule #10: 40S ribosomal protein S19-A
+Macromolecule #11: 40S ribosomal protein S20
+Macromolecule #12: 40S ribosomal protein S25-A
+Macromolecule #13: 40S ribosomal protein S28-A
+Macromolecule #14: 40S ribosomal protein S29-A
+Macromolecule #15: Ubiquitin-40S ribosomal protein S31
+Macromolecule #16: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #17: 40S ribosomal protein S0-A
+Macromolecule #18: 40S ribosomal protein S1-A
+Macromolecule #19: 40S ribosomal protein S2
+Macromolecule #20: 40S ribosomal protein S4-A
+Macromolecule #21: 40S ribosomal protein S6-A
+Macromolecule #22: 40S ribosomal protein S7-A
+Macromolecule #23: 40S ribosomal protein S8-A
+Macromolecule #24: 40S ribosomal protein S9-A
+Macromolecule #25: 40S ribosomal protein S11-A
+Macromolecule #26: 40S ribosomal protein S13
+Macromolecule #27: 40S ribosomal protein S14-B
+Macromolecule #28: 40S ribosomal protein S21-A
+Macromolecule #29: 40S ribosomal protein S22-A
+Macromolecule #30: 40S ribosomal protein S23-A
+Macromolecule #31: 40S ribosomal protein S24-A
+Macromolecule #32: 40S ribosomal protein S26-B
+Macromolecule #33: 40S ribosomal protein S27-A
+Macromolecule #34: 40S ribosomal protein S30-A
+Macromolecule #35: Multiprotein-bridging factor 1
+Macromolecule #42: 60S ribosomal protein L2-A
+Macromolecule #43: 60S ribosomal protein L3
+Macromolecule #44: 60S ribosomal protein L4-A
+Macromolecule #45: 60S ribosomal protein L5
+Macromolecule #46: 60S ribosomal protein L6-B
+Macromolecule #47: 60S ribosomal protein L7-A
+Macromolecule #48: 60S ribosomal protein L8-A
+Macromolecule #49: 60S ribosomal protein L9-A
+Macromolecule #50: 60S ribosomal protein L10
+Macromolecule #51: 60S ribosomal protein L11-B
+Macromolecule #52: 60S ribosomal protein L13-A
+Macromolecule #53: 60S ribosomal protein L14-A
+Macromolecule #54: 60S ribosomal protein L15-A
+Macromolecule #55: 60S ribosomal protein L16-A
+Macromolecule #56: 60S ribosomal protein L17-A
+Macromolecule #57: 60S ribosomal protein L18-A
+Macromolecule #58: 60S ribosomal protein L19-A
+Macromolecule #59: 60S ribosomal protein L20-A
+Macromolecule #60: 60S ribosomal protein L21-A
+Macromolecule #61: 60S ribosomal protein L22-A
+Macromolecule #62: 60S ribosomal protein L23-A
+Macromolecule #63: 60S ribosomal protein L24-A
+Macromolecule #64: 60S ribosomal protein L25
+Macromolecule #65: 60S ribosomal protein L26-A
+Macromolecule #66: 60S ribosomal protein L27-A
+Macromolecule #67: 60S ribosomal protein L28
+Macromolecule #68: 60S ribosomal protein L29
+Macromolecule #69: 60S ribosomal protein L30
+Macromolecule #70: 60S ribosomal protein L31-A
+Macromolecule #71: 60S ribosomal protein L32
+Macromolecule #72: 60S ribosomal protein L33-A
+Macromolecule #73: 60S ribosomal protein L34-A
+Macromolecule #74: 60S ribosomal protein L35-A
+Macromolecule #75: 60S ribosomal protein L36-A
+Macromolecule #76: 60S ribosomal protein L37-A
+Macromolecule #77: 60S ribosomal protein L38
+Macromolecule #78: 60S ribosomal protein L39
+Macromolecule #79: Ubiquitin-60S ribosomal protein L40
+Macromolecule #80: 60S ribosomal protein L41-B
+Macromolecule #81: 60S ribosomal protein L42-A
+Macromolecule #82: 60S ribosomal protein L43-A
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 300.0 nm |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 2.5 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
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7nrd: |