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Yorodumi- EMDB-7836: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-si... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7836 | |||||||||
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Title | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1. | |||||||||
Map data | post processed map with Bfactor -30 and low pass filtered to 7A with Chimera | |||||||||
Sample |
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Function / homology | Function and homology information Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / translational elongation / Uptake and function of diphtheria toxin / Peptide chain elongation / Protein methylation / hematopoietic progenitor cell differentiation / translation elongation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / translational elongation / Uptake and function of diphtheria toxin / Peptide chain elongation / Protein methylation / hematopoietic progenitor cell differentiation / translation elongation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / positive regulation of translation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / secretory granule lumen / ficolin-1-rich granule lumen / rRNA binding / ribosome / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / GTPase activity / synapse / Neutrophil degranulation / GTP binding / nucleolus / protein kinase binding / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Homo sapiens (human) / Escherichia coli (E. coli) / Cricket paralysis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Pisareva VP / Pisarev AV / Fernandez IS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2018 Title: Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. Authors: Vera P Pisareva / Andrey V Pisarev / Israel S Fernández / Abstract: Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its ...Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome hijacking is achieved by a sophisticated use of molecular mimicry to tRNA and mRNA, employed to manipulate intrinsically dynamic components of the ribosome. Binding and translocation through the ribosome is required for this IRES to initiate translation. We report two structures, solved by single particle electron cryo-microscopy (cryoEM), of a double translocated CrPV-IRES with aminoacyl-tRNA in the peptidyl site (P site) of the ribosome. CrPV-IRES adopts a previously unseen conformation, mimicking the acceptor stem of a canonical E site tRNA. The structures suggest a mechanism for the positioning of the first aminoacyl-tRNA shared with the distantly related Hepatitis C Virus IRES. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7836.map.gz | 184 MB | EMDB map data format | |
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Header (meta data) | emd-7836-v30.xml emd-7836.xml | 96.2 KB 96.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7836_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_7836.png | 187 KB | ||
Masks | emd_7836_msk_1.map | 244.1 MB | Mask map | |
Others | emd_7836_additional.map.gz emd_7836_half_map_1.map.gz emd_7836_half_map_2.map.gz | 193.5 MB 194.7 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7836 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7836 | HTTPS FTP |
-Related structure data
Related structure data | 6d9jMC 7834C 6d90C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7836.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 with Bfactor -30 and low pass filtered to 7A with Chimera | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7836_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_7836_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_7836_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_7836_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mammalian 80S ribosome in complex with translocated CrPV IRES, P-...
+Supramolecule #1: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-...
+Macromolecule #1: uL2
+Macromolecule #2: uL3
+Macromolecule #3: uL4
+Macromolecule #4: uL18
+Macromolecule #5: eL6
+Macromolecule #6: uL30
+Macromolecule #7: eL8
+Macromolecule #8: uL6
+Macromolecule #9: uL16
+Macromolecule #10: uL11
+Macromolecule #11: eL13
+Macromolecule #12: eL14
+Macromolecule #13: eL15
+Macromolecule #14: uL13
+Macromolecule #15: uL22
+Macromolecule #16: eL18
+Macromolecule #17: eL19
+Macromolecule #18: eL20
+Macromolecule #19: eL21
+Macromolecule #20: eL22
+Macromolecule #21: uL14
+Macromolecule #22: eL24
+Macromolecule #23: eL23
+Macromolecule #24: uL24
+Macromolecule #25: eL27
+Macromolecule #26: uL15
+Macromolecule #27: eL29
+Macromolecule #28: eL30
+Macromolecule #29: eL31
+Macromolecule #30: eL32
+Macromolecule #31: eL33
+Macromolecule #32: eL34
+Macromolecule #33: eL35
+Macromolecule #34: eL36
+Macromolecule #35: eL37
+Macromolecule #36: eL38
+Macromolecule #37: eL39
+Macromolecule #38: eL40
+Macromolecule #39: eL41
+Macromolecule #40: eL42
+Macromolecule #41: eL43
+Macromolecule #42: eL28
+Macromolecule #43: uL10
+Macromolecule #44: uL11
+Macromolecule #48: uL1
+Macromolecule #50: uS2
+Macromolecule #51: eS1
+Macromolecule #52: uS5
+Macromolecule #53: uS3
+Macromolecule #54: eS4
+Macromolecule #55: uS7
+Macromolecule #56: eS6
+Macromolecule #57: eS7
+Macromolecule #58: eS8
+Macromolecule #59: uS4
+Macromolecule #60: eS10
+Macromolecule #61: uS17
+Macromolecule #62: eS12
+Macromolecule #63: uS15
+Macromolecule #64: uS11
+Macromolecule #65: uS19
+Macromolecule #66: uS9
+Macromolecule #67: eS17
+Macromolecule #68: uS13
+Macromolecule #69: eS19
+Macromolecule #70: uS10
+Macromolecule #71: eS21
+Macromolecule #72: uS8
+Macromolecule #73: uS12
+Macromolecule #74: eS24
+Macromolecule #75: eS25
+Macromolecule #76: eS26
+Macromolecule #77: eS27
+Macromolecule #78: eS28
+Macromolecule #79: eS29
+Macromolecule #80: eS30
+Macromolecule #81: eS31
+Macromolecule #82: RACK1
+Macromolecule #84: eEF2
+Macromolecule #45: 28S rRNA
+Macromolecule #46: 5S rRNA
+Macromolecule #47: 5.8S rRNA
+Macromolecule #49: 18S rRNA
+Macromolecule #83: P-site tRNA
+Macromolecule #85: CrPV IRES
+Macromolecule #86: ZINC ION
+Macromolecule #87: MAGNESIUM 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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |