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Yorodumi- EMDB-7834: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-si... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7834 | |||||||||
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Title | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1. | |||||||||
Map data | post-processed map with B-factor -30 and low pass filter to 4.8A | |||||||||
Sample |
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Function / homology | Function and homology information translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / ribosomal subunit / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / ribosomal subunit / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / translational termination / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / : / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / ribosome binding / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding / 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_7834.map.gz | 37.5 MB | EMDB map data format | |
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Header (meta data) | emd-7834-v30.xml emd-7834.xml | 93.4 KB 93.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7834_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_7834.png | 173.6 KB | ||
Masks | emd_7834_msk_1.map | 244.1 MB | Mask map | |
Others | emd_7834_additional_1.map.gz emd_7834_additional_2.map.gz | 193.6 MB 40.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7834 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7834 | HTTPS FTP |
-Related structure data
Related structure data | 6d90MC 7836C 6d9jC 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_7834.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 B-factor -30 and low pass filter to 4.8A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_7834_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_7834_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post-processed map using autoBfactor option in Relion
File | emd_7834_additional_2.map | ||||||||||||
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Annotation | post-processed map using autoBfactor option in Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mammalian 80S ribosome in complex with a double translocated CrPV...
+Supramolecule #1: Mammalian 80S ribosome in complex with a double translocated CrPV...
+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: rL18
+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 #51: uS2
+Macromolecule #52: eS1
+Macromolecule #53: uS5
+Macromolecule #54: uS3
+Macromolecule #55: eS4
+Macromolecule #56: uS7
+Macromolecule #57: eS6
+Macromolecule #58: eS7
+Macromolecule #59: eS8
+Macromolecule #60: uS4
+Macromolecule #61: eS10
+Macromolecule #62: uS17
+Macromolecule #63: eS12
+Macromolecule #64: uS15
+Macromolecule #65: uS11
+Macromolecule #66: uS19
+Macromolecule #67: uS9
+Macromolecule #68: eS17
+Macromolecule #69: uS13
+Macromolecule #70: eS19
+Macromolecule #71: uS10
+Macromolecule #72: eS21
+Macromolecule #73: uS8
+Macromolecule #74: uS12
+Macromolecule #75: eS24
+Macromolecule #76: eS25
+Macromolecule #77: eS26
+Macromolecule #78: eS27
+Macromolecule #79: eS28
+Macromolecule #80: eS29
+Macromolecule #81: eS30
+Macromolecule #82: eS31
+Macromolecule #83: RACK1
+Macromolecule #84: eRF1
+Macromolecule #45: 28S rRNA
+Macromolecule #46: 5S rRNA
+Macromolecule #47: 5.8S rRNA
+Macromolecule #49: 18S rRNA
+Macromolecule #50: P-tRNA
+Macromolecule #85: CrPV-IRES
-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 |