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Yorodumi- EMDB-25534: Structure of the HCV IRES bound to the 40S ribosomal subunit, hea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25534 | |||||||||||||||
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Title | Structure of the HCV IRES bound to the 40S ribosomal subunit, head opening. Structure 8(delta dII) | |||||||||||||||
Map data | Post processed map | |||||||||||||||
Sample |
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Function / homology | Function and homology information ribosomal subunit / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...ribosomal subunit / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / erythrocyte development / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of 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 / cellular response to leukemia inhibitory factor / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / virus receptor activity / small ribosomal subunit / T cell differentiation in thymus / cell body / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cytosolic large ribosomal subunit / mitochondrial inner membrane / cell differentiation / postsynaptic density / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / synapse / negative regulation of apoptotic process / nucleolus / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / rabbit (rabbit) / Hepatitis C virus (isolate 1) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 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_25534.map.gz | 228.1 MB | EMDB map data format | |
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Header (meta data) | emd-25534-v30.xml emd-25534.xml | 56.6 KB 56.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25534_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_25534.png | 37.1 KB | ||
Masks | emd_25534_msk_1.map | 244.1 MB | Mask map | |
Others | emd_25534_additional_1.map.gz emd_25534_additional_2.map.gz emd_25534_additional_3.map.gz emd_25534_half_map_1.map.gz emd_25534_half_map_2.map.gz | 122.9 MB 143.3 MB 192.4 MB 193.7 MB 193.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25534 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25534 | HTTPS FTP |
-Validation report
Summary document | emd_25534_validation.pdf.gz | 972 KB | Display | EMDB validaton report |
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Full document | emd_25534_full_validation.pdf.gz | 971.6 KB | Display | |
Data in XML | emd_25534_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | emd_25534_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25534 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25534 | HTTPS FTP |
-Related structure data
Related structure data | 7synMC 7sygC 7syhC 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_25534.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_25534_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Local resolution values
File | emd_25534_additional_1.map | ||||||||||||
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Annotation | Local resolution values | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local resolution map filtered at local resolution
File | emd_25534_additional_2.map | ||||||||||||
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Annotation | Local resolution map filtered at local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_25534_additional_3.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_25534_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_25534_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
+Supramolecule #1: 40S ribosomal small subunit with HCV IRES
+Macromolecule #1: 18S rRNA
+Macromolecule #36: HCV IRES
+Macromolecule #2: uS2 (SA)
+Macromolecule #3: eS1
+Macromolecule #4: 40S ribosomal protein S2
+Macromolecule #5: uS3
+Macromolecule #6: eS4 (S4 X isoform)
+Macromolecule #7: uS7
+Macromolecule #8: eS6
+Macromolecule #9: eS7
+Macromolecule #10: eS8
+Macromolecule #11: uS4
+Macromolecule #12: eS10
+Macromolecule #13: uS17
+Macromolecule #14: eS12
+Macromolecule #15: uS15
+Macromolecule #16: uS11
+Macromolecule #17: uS19
+Macromolecule #18: uS9
+Macromolecule #19: eS17
+Macromolecule #20: uS13
+Macromolecule #21: eS19
+Macromolecule #22: uS10
+Macromolecule #23: eS21
+Macromolecule #24: uS8
+Macromolecule #25: uS12
+Macromolecule #26: eS24
+Macromolecule #27: eS25
+Macromolecule #28: eS26
+Macromolecule #29: eS27
+Macromolecule #30: eS28
+Macromolecule #31: uS14
+Macromolecule #32: eS30
+Macromolecule #33: eS31
+Macromolecule #34: Receptor for Activated C Kinase 1 (RACK1)
+Macromolecule #35: eL41
+Macromolecule #37: ZINC ION
-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 / Pretreatment - Atmosphere: OTHER / Details: H2/O2 mixture for 25 seconds at 25W power |
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) / 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 |