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Yorodumi- EMDB-25601: Map of the wt IRES eIF5B-containing 48S initiation complex, close... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25601 | |||||||||||||||
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Title | Map of the wt IRES eIF5B-containing 48S initiation complex, closed conformation. eIF5B in position 2 | |||||||||||||||
Map data | Post processed map | |||||||||||||||
Sample |
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Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Brown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: To Be Published Title: Molecular architecture of 40S initiation complexes on the Hepatitis C virus IRES: from ribosomal attachment to eIF5B-mediated reorientation of initiator tRNA Authors: Brown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25601.map.gz | 228.4 MB | EMDB map data format | |
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Header (meta data) | emd-25601-v30.xml emd-25601.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25601_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_25601.png | 59.5 KB | ||
Masks | emd_25601_msk_1.map | 244.1 MB | Mask map | |
Others | emd_25601_half_map_1.map.gz emd_25601_half_map_2.map.gz | 194 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25601 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25601 | HTTPS FTP |
-Validation report
Summary document | emd_25601_validation.pdf.gz | 1010.7 KB | Display | EMDB validaton report |
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Full document | emd_25601_full_validation.pdf.gz | 1010.3 KB | Display | |
Data in XML | emd_25601_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_25601_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25601 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25601 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25601.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Post processed map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25601_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_25601_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_25601_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 40S ribosomal small subunit with HCV IRES
Entire | Name: 40S ribosomal small subunit with HCV IRES |
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Components |
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-Supramolecule #1: 40S ribosomal small subunit with HCV IRES
Supramolecule | Name: 40S ribosomal small subunit with HCV IRES / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#36 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.000075 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot time, force 3. |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Sampling interval: 5.0 µm / Average exposure time: 4.0 sec. / Average electron dose: 70.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |