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Yorodumi- PDB-6i0y: TnaC-stalled ribosome complex with the titin I27 domain folding c... -
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-Basic information
Entry | Database: PDB / ID: 6i0y | ||||||
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Title | TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel | ||||||
Components |
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Keywords | RIBOSOME / Protein folding / ribosomal exit tunnel / nascent chain / titin I27 domain | ||||||
Function / homology | Function and homology information positive regulation of tryptophan metabolic process / transcriptional attenuation by ribosome / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / tryptophan catabolic process ...positive regulation of tryptophan metabolic process / transcriptional attenuation by ribosome / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / tryptophan catabolic process / cardiac muscle tissue morphogenesis / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / M band / I band / protein kinase regulator activity / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / stringent response / skeletal muscle thin filament assembly / striated muscle thin filament / condensed nuclear chromosome / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / striated muscle contraction / muscle contraction / cardiac muscle contraction / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / protein kinase A signaling / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / positive regulation of protein secretion / regulation of cell growth / DNA-templated transcription termination / response to calcium ion / response to radiation / mRNA 5'-UTR binding / Z disc / actin filament binding / large ribosomal subunit / Platelet degranulation / ribosome binding / protein tyrosine kinase activity / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / protease binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / calmodulin binding / rRNA binding / non-specific serine/threonine protein kinase / negative regulation of translation / ribosome / structural constituent of ribosome / translation / protein serine kinase activity / response to antibiotic / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / mRNA binding / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Su, T. / Kudva, R. / von Heijne, G. / Beckmann, R. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Folding pathway of an Ig domain is conserved on and off the ribosome. Authors: Pengfei Tian / Annette Steward / Renuka Kudva / Ting Su / Patrick J Shilling / Adrian A Nickson / Jeffrey J Hollins / Roland Beckmann / Gunnar von Heijne / Jane Clarke / Robert B Best / Abstract: Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ...Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-β Ig domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force dependence of escape from arrest accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations-which also reproduce experiments on mutant forms of I27-show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6i0y.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6i0y.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 6i0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i0y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6i0y_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6i0y_validation.xml.gz | 176.5 KB | Display | |
Data in CIF | 6i0y_validation.cif.gz | 288.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i0y ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i0y | HTTPS FTP |
-Related structure data
Related structure data | 0322MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 31 types, 31 molecules h01234568CDEFGHIJKLMNOPQRSTWXYZ
-RNA chain , 3 types, 3 molecules ABV
#11: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1109114233 |
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#12: RNA chain | Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1430654817 |
#31: RNA chain | Mass: 24876.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1476611766 |
-Protein/peptide / Protein , 2 types, 2 molecules 7z
#36: Protein | Mass: 9794.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) / Strain (production host): KC6 References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase |
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#9: Protein/peptide | Mass: 2899.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KC6 / Gene: tnaC, tnaL, b3707, JW3685 / Production host: Escherichia coli (E. coli) / Strain (production host): KC6 / References: UniProt: P0AD89 |
-Non-polymers , 4 types, 584 molecules
#37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-ZN / | #39: Chemical | ChemComp-TRP / | #40: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 0.926 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2613 |
Image scans | Movie frames/image: 30 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 468015 | ||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 301510 / Symmetry type: POINT |