- EMDB-16155: Structure of rabbit 80S ribosome translating beta-tubulin in comp... -
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Basic information
Entry
Database: EMDB / ID: EMD-16155
Title
Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)
Map data
Sharpened map of the 60S subunit bound to SCAPER and TTC5
Sample
Complex: rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)
ooplasm / odontoblast differentiation / positive regulation of mRNA catabolic process / sperm head / cytoskeleton-dependent intracellular transport / GTPase activating protein binding / regulation of G1 to G0 transition / exit from mitosis / 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 ...ooplasm / odontoblast differentiation / positive regulation of mRNA catabolic process / sperm head / cytoskeleton-dependent intracellular transport / GTPase activating protein binding / regulation of G1 to G0 transition / exit from mitosis / 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 / natural killer cell mediated cytotoxicity / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / antral ovarian follicle growth / retinal ganglion cell axon guidance / G1 to G0 transition / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / seminiferous tubule development / MHC class I protein binding / microtubule-based process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein-RNA complex assembly / spindle assembly / negative regulation of ubiquitin-dependent protein catabolic process / cellular response to actinomycin D / rough endoplasmic reticulum / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to starvation / AURKA Activation by TPX2 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / positive regulation of translation / Regulation of TP53 Activity through Methylation / structural constituent of cytoskeleton / cellular response to gamma radiation / mitotic spindle / transcription coactivator binding / mRNA 5'-UTR binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / rRNA processing / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / mitotic cell cycle / cell body / 5S rRNA binding / cytoplasmic vesicle / large ribosomal subunit rRNA binding / spermatogenesis / defense response to Gram-negative bacterium / killing of cells of another organism / microtubule / cytosolic large ribosomal subunit / Potential therapeutics for SARS / nucleic acid binding / cytoplasmic translation / tRNA binding / postsynaptic density / cytoskeleton / protein stabilization / rRNA binding / ribosome / nuclear speck / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / membrane raft / protein domain specific binding / cell division / DNA repair / GTPase activity / mRNA binding / ubiquitin protein ligase binding / synapse / DNA damage response / chromatin binding / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / nucleolus / GTP binding / structural molecule activity Similarity search - Function
S phase cyclin A-associated protein in the endoplasmic reticulum, N-terminal / S phase cyclin A-associated protein in the endoplasmic reticulum / Tetratricopeptide repeat protein 5, OB fold domain / TTC5, OB fold domain superfamily / Tetratricopeptide repeat protein 5 OB fold domain / Zinc-finger of C2H2 type / 60s Acidic ribosomal protein / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 60S acidic ribosomal protein P0 ...S phase cyclin A-associated protein in the endoplasmic reticulum, N-terminal / S phase cyclin A-associated protein in the endoplasmic reticulum / Tetratricopeptide repeat protein 5, OB fold domain / TTC5, OB fold domain superfamily / Tetratricopeptide repeat protein 5 OB fold domain / Zinc-finger of C2H2 type / 60s Acidic ribosomal protein / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 60S acidic ribosomal protein P0 / : / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / : / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein L23, N-terminal domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / Ribosomal protein L6e / Tubulin-beta mRNA autoregulation signal. / TPR repeat region circular profile. / 60S ribosomal protein L6E / Beta tubulin, autoregulation binding site / Ribosomal protein L37ae / Ribosomal L37ae protein family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Beta tubulin / Ribosomal protein L39e / Ribosomal protein L14e domain / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal protein L35Ae / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L14 / Ribosomal protein L6 signature 2. Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 ...Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Tubulin beta chain / Tetratricopeptide repeat protein 5 / S phase cyclin A-associated protein in the endoplasmic reticulum / Large ribosomal subunit protein eL37 Similarity search - Component
Biological species
Oryctolagus cuniculus (rabbit) / rabbit (rabbit) / Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 2.8 Å
United Kingdom, European Union, Germany, Switzerland, United States, 7 items
Organization
Grant number
Country
Medical Research Council (MRC, United Kingdom)
MC_UP_A022_1007
United Kingdom
Medical Research Council (MRC, United Kingdom)
MC_U105192715
United Kingdom
European Molecular Biology Organization (EMBO)
ALTF 116-2020
European Union
H2020 Marie Curie Actions of the European Commission
101029853
European Union
German Research Foundation (DFG)
429892960
Germany
Swiss National Science Foundation
PCEFP3_194312
Switzerland
Damon Runyon Cancer Research Foundation
DRG:2279-16
United States
Citation
Journal: Mol Cell / Year: 2023 Title: Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation. Authors: Markus Höpfler / Eva Absmeier / Sew-Yeu Peak-Chew / Evangelia Vartholomaiou / Lori A Passmore / Ivana Gasic / Ramanujan S Hegde / Abstract: Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits affects polymerization dynamics and microtubule function. ...Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits affects polymerization dynamics and microtubule function. When cells sense excess free tubulin, they trigger degradation of the encoding mRNAs, which requires recognition of the nascent polypeptide by the tubulin-specific ribosome-binding factor TTC5. How TTC5 initiates the decay of tubulin mRNAs is unknown. Here, our biochemical and structural analysis reveals that TTC5 recruits the poorly studied protein SCAPER to the ribosome. SCAPER, in turn, engages the CCR4-NOT deadenylase complex through its CNOT11 subunit to trigger tubulin mRNA decay. SCAPER mutants that cause intellectual disability and retinitis pigmentosa in humans are impaired in CCR4-NOT recruitment, tubulin mRNA degradation, and microtubule-dependent chromosome segregation. Our findings demonstrate how recognition of a nascent polypeptide on the ribosome is physically linked to mRNA decay factors via a relay of protein-protein interactions, providing a paradigm for specificity in cytoplasmic gene regulation.
Entire : rabbit 80S ribosome translating beta-tubulin in complex with tetr...
Entire
Name: rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)
Components
Complex: rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)
RNA: 28S ribosomal RNA
RNA: 5S ribosomal RNA
RNA: 5.8S ribosomal RNA
Protein or peptide: Nascent polypeptide-associated complex subunit alpha N-terminal region
Protein or peptide: 60S ribosomal protein L8
Protein or peptide: Ribosomal protein L3
Protein or peptide: 60S ribosomal protein L4
Protein or peptide: Ribosomal_L18_c domain-containing protein
Protein or peptide: 60S ribosomal protein L6
Protein or peptide: 60S ribosomal protein L7
Protein or peptide: 60S ribosomal protein L7a
Protein or peptide: 60S ribosomal protein L9
Protein or peptide: Ribosomal protein L10
Protein or peptide: 60S ribosomal protein L11
Protein or peptide: 60S ribosomal protein L13
Protein or peptide: 60S ribosomal protein L14
Protein or peptide: Ribosomal protein L15
Protein or peptide: 60S ribosomal protein L13a
Protein or peptide: 60S ribosomal protein L17
Protein or peptide: Ribosomal protein L18
Protein or peptide: 60S ribosomal protein L19
Protein or peptide: 60S ribosomal protein L18a
Protein or peptide: 60S ribosomal protein L21
Protein or peptide: 60S ribosomal protein L22
Protein or peptide: 60S ribosomal protein L23
Protein or peptide: Ribosomal protein L24
Protein or peptide: Ribosomal_L23eN domain-containing protein
Protein or peptide: Ribosomal protein L26
Protein or peptide: 60S ribosomal protein L27
Protein or peptide: 60S ribosomal protein L27a
Protein or peptide: 60S ribosomal protein L29
Protein or peptide: 60S ribosomal protein L30
Protein or peptide: 60S ribosomal protein L31
Protein or peptide: Ribosomal protein L32
Protein or peptide: 60S ribosomal protein L35a
Protein or peptide: 60S ribosomal protein L34
Protein or peptide: 60S ribosomal protein L35
Protein or peptide: 60S ribosomal protein L36
Protein or peptide: Ribosomal protein L37
Protein or peptide: 60S ribosomal protein L38
Protein or peptide: 60S ribosomal protein L39-like
Protein or peptide: Ubiquitin-60S ribosomal protein L40
Protein or peptide: 60S ribosomal protein L41
Protein or peptide: 60S ribosomal protein L36a-like
Protein or peptide: 60S ribosomal protein L37a
Protein or peptide: 60S ribosomal protein L28
Protein or peptide: 60S acidic ribosomal protein P0
Protein or peptide: 60S ribosomal protein L12
Protein or peptide: S phase cyclin A-associated protein in the endoplasmic reticulum
Protein or peptide: Tetratricopeptide repeat protein 5
Protein or peptide: Tubulin beta chain
Ligand: MAGNESIUM ION
Ligand: ZINC ION
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Supramolecule #1: rabbit 80S ribosome translating beta-tubulin in complex with tetr...
Supramolecule
Name: rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#51
Source (natural)
Organism: Oryctolagus cuniculus (rabbit)
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Macromolecule #1: 28S ribosomal RNA
Macromolecule
Name: 28S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Macromolecule #49: S phase cyclin A-associated protein in the endoplasmic reticulum
Macromolecule
Name: S phase cyclin A-associated protein in the endoplasmic reticulum type: protein_or_peptide / ID: 49 Details: First 11 N-terminal residues correspond to a FLAG-tag Number of copies: 1 / Enantiomer: LEVO
UniProtKB: S phase cyclin A-associated protein in the endoplasmic reticulum
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Macromolecule #50: Tetratricopeptide repeat protein 5
Macromolecule
Name: Tetratricopeptide repeat protein 5 / type: protein_or_peptide / ID: 50 Details: The first 49 N-terminal residues correspond to a 6x His and a twin strep tag. Number of copies: 1 / Enantiomer: LEVO
Name: MAGNESIUM ION / type: ligand / ID: 52 / Number of copies: 214 / Formula: MG
Molecular weight
Theoretical: 24.305 Da
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Macromolecule #53: ZINC ION
Macromolecule
Name: ZINC ION / type: ligand / ID: 53 / Number of copies: 5 / Formula: ZN
Molecular weight
Theoretical: 65.409 Da
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.4
Grid
Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 20932 / Average exposure time: 1.8 sec. / Average electron dose: 44.7 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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