- EMDB-53860: Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state -
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Basic information
Entry
Database: EMDB / ID: EMD-53860
Title
Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state
Map data
DeepEMhanced map
Sample
Complex: S. cerevisiae 80S ribosome in a non-rotated, post-translocation state with a P-site tRNA-Met-elongation, a nacent chain (Pgk 1-70), and Ssb1 in the ADP state adapting the S1 conformation
RNA: x 6 types
Protein or peptide: x 73 types
Keywords
Hsp70 / nascent chain / 80S / Ssb / RIBOSOME
Function / homology
Function and homology information
Mitochondrial unfolded protein response (UPRmt) / translational frameshifting / Gluconeogenesis / Glycolysis / 'de novo' cotranslational protein folding / phosphoglycerate kinase / phosphoglycerate kinase activity / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of HSF1-mediated heat shock response ...Mitochondrial unfolded protein response (UPRmt) / translational frameshifting / Gluconeogenesis / Glycolysis / 'de novo' cotranslational protein folding / phosphoglycerate kinase / phosphoglycerate kinase activity / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of HSF1-mediated heat shock response / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / : / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / non-chaperonin molecular chaperone ATPase / negative regulation of mRNA splicing, via spliceosome / : / positive regulation of protein kinase activity / preribosome, large subunit precursor / 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 translational frameshifting / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / translational termination / regulation of translational fidelity / ribosomal subunit export from nucleus / protein-RNA complex assembly / maturation of LSU-rRNA / heat shock protein binding / 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) / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / protein folding chaperone / rescue of stalled cytosolic ribosome / cellular response to amino acid starvation / protein kinase C binding / ribosomal large subunit biogenesis / ribosome assembly / glycolytic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gluconeogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / maturation of SSU-rRNA / ATP-dependent protein folding chaperone / small-subunit processome / translational initiation / ADP binding / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosome binding / protein refolding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / calmodulin binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site ...Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L44e signature. / 40S Ribosomal protein S10 / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site / : / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S25 / S25 ribosomal protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein S2, eukaryotic/archaeal / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal protein S3Ae, conserved site / Ribosomal Protein L6, KOW domain / Ribosomal protein S3Ae signature. / Ribosomal protein L39e, conserved site Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Phosphoglycerate kinase / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein eL6B / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A ...Small ribosomal subunit protein uS4A / Phosphoglycerate kinase / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein eL6B / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Small ribosomal subunit protein eS28B / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32B / Large ribosomal subunit protein uL4A / Ribosome-associated molecular chaperone SSB1 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS17B / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein eL24B / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS26A / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Small ribosomal subunit protein eS25A Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 2.9 Å
Entire : S. cerevisiae 80S ribosome in a non-rotated, post-translocation s...
Entire
Name: S. cerevisiae 80S ribosome in a non-rotated, post-translocation state with a P-site tRNA-Met-elongation, a nacent chain (Pgk 1-70), and Ssb1 in the ADP state adapting the S1 conformation
Components
Complex: S. cerevisiae 80S ribosome in a non-rotated, post-translocation state with a P-site tRNA-Met-elongation, a nacent chain (Pgk 1-70), and Ssb1 in the ADP state adapting the S1 conformation
RNA: mRNA_Flag-Pgk-1-70
RNA: tRNA Methionin elongator
Protein or peptide: Ribosome-associated molecular chaperone SSB1
Protein or peptide: Phosphoglycerate kinase
RNA: 25S ribosomal RNA
RNA: 18S ribosomal RNA
RNA: 5.8S ribosomal RNA
RNA: 5S ribosomal RNA
Protein or peptide: 60S ribosomal protein L2-A
Protein or peptide: 60S ribosomal protein L3
Protein or peptide: 60S ribosomal protein L4-A
Protein or peptide: 60S ribosomal protein L5
Protein or peptide: 60S ribosomal protein L6-B
Protein or peptide: 60S ribosomal protein L7-A
Protein or peptide: 60S ribosomal protein L8-A
Protein or peptide: 60S ribosomal protein L9-A
Protein or peptide: 60S ribosomal protein L10
Protein or peptide: 60S ribosomal protein L11-A
Protein or peptide: 60S ribosomal protein L13-A
Protein or peptide: 60S ribosomal protein L14-A
Protein or peptide: 60S ribosomal protein L15-A
Protein or peptide: 60S ribosomal protein L16-A
Protein or peptide: 60S ribosomal protein L17-A
Protein or peptide: 60S ribosomal protein L18-A
Protein or peptide: 60S ribosomal protein L19-A
Protein or peptide: 60S ribosomal protein L20-A
Protein or peptide: 60S ribosomal protein L21-A
Protein or peptide: 60S ribosomal protein L22-A
Protein or peptide: 60S ribosomal protein L23-A
Protein or peptide: Large ribosomal subunit protein eL24B
Protein or peptide: 60S ribosomal protein L25
Protein or peptide: 60S ribosomal protein L26-A
Protein or peptide: 60S ribosomal protein L27-A
Protein or peptide: 60S ribosomal protein L28
Protein or peptide: 60S ribosomal protein L29
Protein or peptide: 60S ribosomal protein L30
Protein or peptide: 60S ribosomal protein L31-A
Protein or peptide: 60S ribosomal protein L32
Protein or peptide: 60S ribosomal protein L33-A
Protein or peptide: 60S ribosomal protein L34-A
Protein or peptide: 60S ribosomal protein L35-A
Protein or peptide: 60S ribosomal protein L36-A
Protein or peptide: 60S ribosomal protein L37-A
Protein or peptide: 60S ribosomal protein L38
Protein or peptide: 60S ribosomal protein L39
Protein or peptide: Large ribosomal subunit protein eL41B
Protein or peptide: 60S ribosomal protein L42-A
Protein or peptide: 60S ribosomal protein L43-A
Protein or peptide: 40S ribosomal protein S0-A
Protein or peptide: 40S ribosomal protein S1-A
Protein or peptide: 40S ribosomal protein S2
Protein or peptide: Small ribosomal subunit protein uS3
Protein or peptide: 40S ribosomal protein S4-A
Protein or peptide: 40S ribosomal protein S5
Protein or peptide: 40S ribosomal protein S6-A
Protein or peptide: 40S ribosomal protein S7-A
Protein or peptide: 40S ribosomal protein S8-A
Protein or peptide: 40S ribosomal protein S9-A
Protein or peptide: 40S ribosomal protein S10-A
Protein or peptide: 40S ribosomal protein S11-A
Protein or peptide: 40S ribosomal protein S13
Protein or peptide: 40S ribosomal protein S14-A
Protein or peptide: 40S ribosomal protein S15
Protein or peptide: 40S ribosomal protein S16-A
Protein or peptide: 40S ribosomal protein S17-B
Protein or peptide: 40S ribosomal protein S18-A
Protein or peptide: 40S ribosomal protein S19-A
Protein or peptide: Small ribosomal subunit protein uS10
Protein or peptide: 40S ribosomal protein S21-A
Protein or peptide: 40S ribosomal protein S22-A
Protein or peptide: 40S ribosomal protein S23-A
Protein or peptide: 40S ribosomal protein S24-A
Protein or peptide: 40S ribosomal protein S25-A
Protein or peptide: Small ribosomal subunit protein eS26A
Protein or peptide: 40S ribosomal protein S27-A
Protein or peptide: Small ribosomal subunit protein eS28B
Protein or peptide: Small ribosomal subunit protein uS14A
Protein or peptide: 40S ribosomal protein S30-A
Protein or peptide: Guanine nucleotide-binding protein subunit beta-like protein
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Supramolecule #1: S. cerevisiae 80S ribosome in a non-rotated, post-translocation s...
Supramolecule
Name: S. cerevisiae 80S ribosome in a non-rotated, post-translocation state with a P-site tRNA-Met-elongation, a nacent chain (Pgk 1-70), and Ssb1 in the ADP state adapting the S1 conformation type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#79
Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE
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Electron microscopy
Microscope
TFS KRIOS
Specialist optics
Energy filter - Name: TFS Selectris X
Image recording
Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 54286 / Average electron dose: 40.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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