[English] 日本語
![](img/lk-miru.gif)
- EMDB-25531: Structure of the HCV IRES binding to the 40S ribosomal subunit, c... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the HCV IRES binding to the 40S ribosomal subunit, closed conformation. Structure 5(delta dII) | |||||||||||||||
![]() | Post processed map | |||||||||||||||
![]() |
| |||||||||||||||
![]() | HCV / IRES / 40S / RIBOSOME | |||||||||||||||
Function / homology | ![]() laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response ...laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / G1/S transition of mitotic cell cycle / protein tag activity / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / glucose homeostasis / regulation of translation / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / mitochondrial inner membrane / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / 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 | ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
![]() | Brown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. Authors: Zuben P Brown / Irina S Abaeva / Swastik De / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / ![]() Abstract: Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical ...Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining. | |||||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 227.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 60.2 KB 60.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 35.9 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 12.5 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 144.8 MB 122.6 MB 193.6 MB 194.1 MB 193.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sykMC ![]() 7syiC ![]() 7syjC ![]() 7sylC ![]() 7syoC ![]() 7sypC ![]() 7syqC ![]() 7syrC ![]() 7sysC ![]() 7sytC ![]() 7syuC ![]() 7syvC ![]() 7sywC ![]() 7syxC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post processed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Local resolution map filtered at local resolution
File | emd_25531_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Local resolution map filtered at local resolution | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Local resolution values
File | emd_25531_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Local resolution values | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened map
File | emd_25531_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map
File | emd_25531_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map
File | emd_25531_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map | ||||||||||||
Projections & Slices |
| ||||||||||||
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: 40S ribosomal protein SA
+Macromolecule #3: eS1
+Macromolecule #4: uS5 (S2)
+Macromolecule #5: uS3
+Macromolecule #6: 40S ribosomal protein S4
+Macromolecule #7: uS7
+Macromolecule #8: eS6
+Macromolecule #9: 40S ribosomal protein S7
+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: 40S ribosomal protein S21
+Macromolecule #24: uS8
+Macromolecule #25: uS12
+Macromolecule #26: 40S ribosomal protein S24
+Macromolecule #27: eS25 (S25)
+Macromolecule #28: eS26 (S26)
+Macromolecule #29: eS27
+Macromolecule #30: eS28
+Macromolecule #31: eS29
+Macromolecule #32: eS30
+Macromolecule #33: 40S ribosomal protein S27a
+Macromolecule #34: RACK1
+Macromolecule #35: 60s ribosomal protein l41
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.000075 mg/mL |
---|---|
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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / 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 |
---|---|
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: ![]() |
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 |