[English] 日本語
Yorodumi- PDB-8bpo: Structure of rabbit 80S ribosome translating beta-tubulin in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bpo | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||
Keywords | RIBOSOME / tubulin auto-regulation mRNA decay translation SCAPER | ||||||||||||||||||||||||
Function / homology | Function and homology information ooplasm / odontoblast differentiation / positive regulation of mRNA catabolic process / sperm head / cytoskeleton-dependent intracellular transport / natural killer cell mediated cytotoxicity / 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 ...ooplasm / odontoblast differentiation / positive regulation of mRNA catabolic process / sperm head / cytoskeleton-dependent intracellular transport / natural killer cell mediated cytotoxicity / 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 / 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 / seminiferous tubule development / nuclear envelope lumen / 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 / 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 / negative regulation of ubiquitin-dependent protein catabolic process / 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 / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / mitotic cell cycle / cell body / 5S rRNA binding / large ribosomal subunit rRNA binding / cytoplasmic vesicle / spermatogenesis / defense response to Gram-negative bacterium / microtubule / killing of cells of another organism / Potential therapeutics for SARS / nucleic acid binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / 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 / protein-containing complex binding / positive regulation of gene expression / nucleolus / GTP binding / structural molecule activity Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||||||||
Authors | Hopfler, M. / Absmeier, E. / Passmore, L.A. / Hegde, R.S. | ||||||||||||||||||||||||
Funding support | United Kingdom, European Union, Germany, Switzerland, United States, 7items
| ||||||||||||||||||||||||
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. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bpo.cif.gz | 3.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bpo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bpo_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8bpo_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8bpo_validation.xml.gz | 241.7 KB | Display | |
Data in CIF | 8bpo_validation.cif.gz | 415.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpo ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpo | HTTPS FTP |
-Related structure data
Related structure data | 16155MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 3 types, 3 molecules A1B1C1
#1: RNA chain | Mass: 1418701.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
---|---|
#2: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4 |
#3: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_3 |
-Protein/peptide , 1 types, 1 molecules D1
#4: Protein/peptide | Mass: 2526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
---|
+60S ribosomal protein ... , 32 types, 32 molecules A2C2E2F2G2H2J2K2L2N2O2Q2R2S2T2U2Y2Z2a2b2c2e2f2g2h2j2k2m2n2o2p2r2
-Ribosomal protein ... , 8 types, 8 molecules B2I2M2P2V2X2d2i2
#6: Protein | Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06 |
---|---|
#13: Protein | Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2 |
#17: Protein | Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1 |
#20: Protein | Mass: 21568.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#26: Protein | Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28 |
#28: Protein | Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0 |
#34: Protein | Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437 |
#39: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5 |
-Protein , 7 types, 7 molecules D2W2l2q2s2t2u2
#8: Protein | Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6 |
---|---|
#27: Protein | Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76 |
#42: Protein | Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#47: Protein | Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4 |
#49: Protein | Mass: 159795.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First 11 N-terminal residues correspond to a FLAG-tag Source: (gene. exp.) Homo sapiens (human) / Gene: SCAPER, KIAA1454, ZNF291, MSTP063 / Production host: Homo sapiens (human) / References: UniProt: Q9BY12 |
#50: Protein | Mass: 54176.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first 49 N-terminal residues correspond to a 6x His and a twin strep tag. Source: (gene. exp.) Homo sapiens (human) / Gene: TTC5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N0Z6 |
#51: Protein | Mass: 7163.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB, TUBB5, OK/SW-cl.56 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P07437 |
-Non-polymers , 2 types, 219 molecules
#52: Chemical | ChemComp-MG / #53: Chemical | ChemComp-ZN / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | 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: RIBOSOME / Entity ID: #1-#51 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 44.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20932 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1227269 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18949 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.79 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
|