+Open data
-Basic information
Entry | Database: PDB / ID: 8i7j | ||||||
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Title | Yeast 40S-eIF4B - partially open conformation of the 40S head | ||||||
Components |
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Keywords | RIBOSOME | ||||||
Function / homology | Function and homology information endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / translation regulator activity / 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) / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / translation regulator activity / 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) / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Kluyveromyces lactis NRRL Y-1140 (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Datey, A. / Khaja, F.T. / Hussain, T. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Yeast eukaryotic initiation factor 4B remodels the mRNA entry site on the small ribosomal subunit Authors: Datey, A. / Hussain, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i7j.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8i7j.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8i7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i7j_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8i7j_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8i7j_validation.xml.gz | 143.7 KB | Display | |
Data in CIF | 8i7j_validation.cif.gz | 252.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/8i7j ftp://data.pdbj.org/pub/pdb/validation_reports/i7/8i7j | HTTPS FTP |
-Related structure data
Related structure data | 35216MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-40S ribosomal protein ... , 17 types, 17 molecules ABEGHIMOQVYZabcde
#2: Protein | Mass: 28264.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CN12 |
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#3: Protein | Mass: 28971.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWD0 |
#6: Protein | Mass: 29617.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWJ2 |
#8: Protein | Mass: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CM04 |
#9: Protein | Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CTD6 |
#10: Protein | Mass: 22642.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CMG3 |
#14: Protein | Mass: 14466.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CLU4 |
#16: Protein | Mass: 14530.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: P27069 |
#18: Protein | Mass: 15874.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q875N2 |
#23: Protein | Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CXT6 |
#26: Protein | Mass: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CU44 |
#27: Protein | Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CW78 |
#28: Protein | Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CS01 |
#29: Protein | Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CNL2 |
#30: Protein | Mass: 7549.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: P33285 |
#31: Protein | Mass: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CPG3 |
#32: Protein | Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CUH5 |
-Protein , 16 types, 16 molecules CDFJKLNPRSTUWXfg
#4: Protein | Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CKL3 |
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#5: Protein | Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CRK7 |
#7: Protein | Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CRA3 |
#11: Protein | Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CM18 |
#12: Protein | Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CVZ5 |
#13: Protein | Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CX80 |
#15: Protein | Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CJK0 |
#17: Protein | Mass: 15986.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CKV4 |
#19: Protein | Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWU3 |
#20: Protein | Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWT9 |
#21: Protein | Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CXM0 |
#22: Protein | Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CIM1 |
#24: Protein | Mass: 14645.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CW06 |
#25: Protein | Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: F2Z602 |
#33: Protein | Mass: 17110.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: P69061 |
#34: Protein | Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CNI7 |
-RNA chain / Protein/peptide , 2 types, 2 molecules 2h
#1: RNA chain | Mass: 579545.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 |
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#35: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: RPL41A / Production host: Escherichia coli (E. coli) / References: UniProt: P0CX86 |
-Non-polymers , 2 types, 5 molecules
#36: Chemical | #37: Chemical | |
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-Details
Has ligand of interest | N |
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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
Component |
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Molecular weight |
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Source (natural) | Cellular location: cytoplasm
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Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta(DE3)pLysS / Plasmid: pTYB2 | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 Details: 20 mM HEPES pH7.4, 100 mM potassium acetate pH7.6, 2.5 mM Magnesium acetate, 2 mM DTT | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This class of empty or only 40S was a part of the reaction mixture containing 40S and the Saccharomyces cerevisiae eukaryotic initiation factor 4B present in a 1:10 molar ratio | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: Vitrification was carried out in nitrogen atmosphere. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA Details: Preliminary grid screening was done manually using the Latitude-S |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: DIFFRACTION / Nominal magnification: 42000 X / Calibrated magnification: 42000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: OTHER |
Specimen holder | Cryogen: NITROGEN / Temperature (max): 98 K / Temperature (min): 77 K |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 6 / Num. of real images: 7975 Details: Images were collected in movie-mode at 20 frames in 8 seconds |
Image scans | Movie frames/image: 20 / Used frames/image: 4-16 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1492547 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108616 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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