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Yorodumi- EMDB-9239: Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9239 | |||||||||
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Title | Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) | |||||||||
Map data | Postprocessed map | |||||||||
Sample |
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Function / homology | Function and homology information ribosomal subunit / regulation of G1 to G0 transition / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition ...ribosomal subunit / regulation of G1 to G0 transition / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / positive regulation of mitochondrial depolarization / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit export from nucleus / translation regulator activity / cellular response to actinomycin D / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / rough endoplasmic reticulum / gastrulation / signaling adaptor activity / MDM2/MDM4 family protein binding / rescue of stalled ribosome / negative regulation of smoothened signaling pathway / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin-dependent protein catabolic process / cytosolic ribosome / negative regulation of peptidyl-serine phosphorylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / ribosomal large subunit biogenesis / small-subunit processome / SH2 domain binding / cyclin binding / positive regulation of translation / protein kinase C binding / : / cellular response to glucose stimulus / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / transcription coactivator binding / negative regulation of cell growth / receptor tyrosine kinase binding / cellular response to growth factor stimulus / rRNA processing / positive regulation of canonical Wnt signaling pathway / cytosolic small ribosomal subunit / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome binding / large ribosomal subunit / cell body / 5S rRNA binding / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / midbody / protein phosphatase binding / cell differentiation / protein stabilization / ribosome / rRNA binding / protein ubiquitination / regulation of cell cycle / structural constituent of ribosome / positive regulation of cell migration / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / negative regulation of gene expression / centrosome / dendrite / synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / nucleolus / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Brown A / Baird MR / Yip MCJ / Murray J / Shao S | |||||||||
Citation | Journal: Elife / Year: 2018 Title: Structures of translationally inactive mammalian ribosomes. Authors: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao / Abstract: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression. | |||||||||
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_9239.map.gz | 16.4 MB | EMDB map data format | |
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Header (meta data) | emd-9239-v30.xml emd-9239.xml | 96.6 KB 96.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9239_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_9239.png | 174.1 KB | ||
Others | emd_9239_additional.map.gz emd_9239_half_map_1.map.gz emd_9239_half_map_2.map.gz | 214.8 MB 215.2 MB 214.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9239 | HTTPS FTP |
-Related structure data
Related structure data | 6mtcMC 9234C 9235C 9236C 9237C 9240C 9241C 9242C 6mtbC 6mtdC 6mteC C: citing same article (ref.) M: atomic model generated by this map |
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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_9239.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Pre-postprocessed map
File | emd_9239_additional.map | ||||||||||||
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Annotation | Pre-postprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_9239_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_9239_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rabbit 80S ribosome with Z-site tRNA and IFRD2
+Supramolecule #1: Rabbit 80S ribosome with Z-site tRNA and IFRD2
+Macromolecule #1: Z-site tRNA
+Macromolecule #2: 28S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #49: 18S rRNA
+Macromolecule #5: 60S ribosomal protein L8
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L6
+Macromolecule #10: 60S ribosomal protein L7
+Macromolecule #11: 60S ribosomal protein L7a
+Macromolecule #12: 60S ribosomal protein L9
+Macromolecule #13: 60S ribosomal protein L10
+Macromolecule #14: 60S ribosomal protein L11
+Macromolecule #15: 60S ribosomal protein L13
+Macromolecule #16: 60S ribosomal protein L14
+Macromolecule #17: 60S Ribosomal protein L15
+Macromolecule #18: 60S ribosomal protein L13a
+Macromolecule #19: 60S ribosomal protein L17
+Macromolecule #20: 60S ribosomal protein L18
+Macromolecule #21: 60S ribosomal protein L19
+Macromolecule #22: 60S ribosomal protein L18a
+Macromolecule #23: 60S ribosomal protein L21
+Macromolecule #24: 60S ribosomal protein L22
+Macromolecule #25: 60S ribosomal protein L23
+Macromolecule #26: 60S ribosomal protein L24
+Macromolecule #27: 60S ribosomal protein L23a
+Macromolecule #28: 60S ribosomal protein L26
+Macromolecule #29: 60S ribosomal protein L27
+Macromolecule #30: 60S ribosomal protein L27a
+Macromolecule #31: 60S ribosomal protein L29
+Macromolecule #32: 60S ribosomal protein L30
+Macromolecule #33: 60S ribosomal protein L31
+Macromolecule #34: 60S ribosomal protein L32
+Macromolecule #35: 60S ribosomal protein L35a
+Macromolecule #36: 60S ribosomal protein L34
+Macromolecule #37: 60S ribosomal protein L35
+Macromolecule #38: 60S ribosomal protein L36
+Macromolecule #39: 60S ribosomal protein L37
+Macromolecule #40: 60S ribosomal protein L38
+Macromolecule #41: 60S ribosomal protein L39
+Macromolecule #42: 60S ribosomal protein L40
+Macromolecule #43: 60S ribosomal protein L41
+Macromolecule #44: 60S ribosomal protein L36a
+Macromolecule #45: 60S ribosomal protein L37a
+Macromolecule #46: 60S ribosomal protein L28
+Macromolecule #47: 60S ribosomal protein L10a
+Macromolecule #48: Interferon-related developmental regulator 2
+Macromolecule #50: 40S ribosomal protein SA
+Macromolecule #51: 40S ribosomal protein S3a
+Macromolecule #52: 40S ribosomal protein S2
+Macromolecule #53: 40S ribosomal protein S3
+Macromolecule #54: 40S ribosomal protein S4, X isoform
+Macromolecule #55: 40S ribosomal protein S5
+Macromolecule #56: 40S ribosomal protein S6
+Macromolecule #57: 40S ribosomal protein S7
+Macromolecule #58: 40S ribosomal protein S8
+Macromolecule #59: 40S ribosomal protein S9
+Macromolecule #60: 40S ribosomal protein S10
+Macromolecule #61: 40S ribosomal protein S11
+Macromolecule #62: 40S ribosomal protein S12
+Macromolecule #63: 40S ribosomal protein S13
+Macromolecule #64: 40S ribosomal protein S14
+Macromolecule #65: 40S ribosomal protein S15
+Macromolecule #66: 40S ribosomal protein S16
+Macromolecule #67: 40S ribosomal protein S17
+Macromolecule #68: 40S ribosomal protein S18
+Macromolecule #69: 40S ribosomal protein S19
+Macromolecule #70: 40S ribosomal protein S20
+Macromolecule #71: 40S ribosomal protein S21
+Macromolecule #72: 40S ribosomal protein S15a
+Macromolecule #73: 40S ribosomal protein S23
+Macromolecule #74: 40S ribosomal protein S24
+Macromolecule #75: 40S ribosomal protein S25
+Macromolecule #76: 40S ribosomal protein S26
+Macromolecule #77: 40S ribosomal protein S27
+Macromolecule #78: 40S ribosomal protein S28
+Macromolecule #79: 40S ribosomal protein S29
+Macromolecule #80: 40S ribosomal protein S30
+Macromolecule #81: 40S ribosomal protein S27a
+Macromolecule #82: Receptor of activated protein C kinase 1
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: ZINC 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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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-17 / Average exposure time: 1.1 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |