+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35216 | |||||||||
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Title | Yeast 40S-eIF4B - partially open conformation of the 40S head | |||||||||
Map data | This is the cryo-EM map of the 40S-eIF4B complex from yeast. | |||||||||
Sample |
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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 / 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 / positive regulation of apoptotic signaling pathway ...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 / 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 / positive regulation of apoptotic signaling pathway / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Kluyveromyces lactis Saccharomyces cerevisiae S288c (yeast) / Kluyveromyces lactis NRRL Y-1140 (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Datey A / Khaja FT / Hussain T | |||||||||
Funding support | India, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35216.map.gz | 166.8 MB | EMDB map data format | |
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Header (meta data) | emd-35216-v30.xml emd-35216.xml | 64.9 KB 64.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35216_fsc.xml | 16.5 KB | Display | FSC data file |
Images | emd_35216.png | 45.8 KB | ||
Filedesc metadata | emd-35216.cif.gz | 12.7 KB | ||
Others | emd_35216_additional_1.map.gz emd_35216_half_map_1.map.gz emd_35216_half_map_2.map.gz | 139 MB 140.7 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35216 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35216 | HTTPS FTP |
-Validation report
Summary document | emd_35216_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_35216_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_35216_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | emd_35216_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35216 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35216 | HTTPS FTP |
-Related structure data
Related structure data | 8i7jMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35216.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | This is the cryo-EM map of the 40S-eIF4B complex from yeast. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.17 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: auto-refined map of the 40S-eIF4B complex
File | emd_35216_additional_1.map | ||||||||||||
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Annotation | auto-refined map of the 40S-eIF4B complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2 of the 40S-eIF4B complex
File | emd_35216_half_map_1.map | ||||||||||||
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Annotation | Half-map 2 of the 40S-eIF4B complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1 of the 40S-eIF4B complex
File | emd_35216_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 of the 40S-eIF4B complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The binary complex of the yeast 40S small ribosomal subunit with ...
+Supramolecule #1: The binary complex of the yeast 40S small ribosomal subunit with ...
+Supramolecule #2: Eukaryotic Initiation Factor 4B (eIF4B).
+Supramolecule #3: yeast 40S small ribosomal subunit
+Macromolecule #1: RNA (1780-MER)
+Macromolecule #2: 40S ribosomal protein S0
+Macromolecule #3: 40S ribosomal protein S1
+Macromolecule #4: KLLA0F09812p
+Macromolecule #5: KLLA0D08305p
+Macromolecule #6: 40S ribosomal protein S4
+Macromolecule #7: KLLA0D10659p
+Macromolecule #8: 40S ribosomal protein S6
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: 40S ribosomal protein S8
+Macromolecule #11: KLLA0E23673p
+Macromolecule #12: KLLA0B08173p
+Macromolecule #13: KLLA0A10483p
+Macromolecule #14: 40S ribosomal protein S12
+Macromolecule #15: KLLA0F18040p
+Macromolecule #16: 40S ribosomal protein S14
+Macromolecule #17: KLLA0F07843p
+Macromolecule #18: 40S ribosomal protein S16
+Macromolecule #19: KLLA0B01474p
+Macromolecule #20: KLLA0B01562p
+Macromolecule #21: KLLA0A07194p
+Macromolecule #22: KLLA0F25542p
+Macromolecule #23: 40S ribosomal protein S21
+Macromolecule #24: KLLA0B07931p
+Macromolecule #25: KLLA0B11231p
+Macromolecule #26: 40S ribosomal protein S24
+Macromolecule #27: 40S ribosomal protein S25
+Macromolecule #28: 40S ribosomal protein S26
+Macromolecule #29: 40S ribosomal protein S27
+Macromolecule #30: 40S ribosomal protein S28
+Macromolecule #31: 40S ribosomal protein S29
+Macromolecule #32: 40S ribosomal protein S30
+Macromolecule #33: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #34: KLLA0E12277p
+Macromolecule #35: 60S ribosomal protein L41-A
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: 20 mM HEPES pH7.4, 100 mM potassium acetate pH7.6, 2.5 mM Magnesium acetate, 2 mM DTT | |||||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 100.0 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: Vitrification was carried out in nitrogen atmosphere.. | |||||||||||||||
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 |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 77.0 K / Max: 98.0 K |
Details | Preliminary grid screening was done manually using the Latitude-S |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 4-16 / Number grids imaged: 6 / Number real images: 7975 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 Details: Images were collected in movie-mode at 20 frames in 8 seconds |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 42000 / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
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Output model | PDB-8i7j: |