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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | 80S ribosome of WT EBV infected human B-cells | |||||||||
Map data | Composite map of 80S ribosomes from primary B-cells infected with WT M81 Epstein-Barr virus. | |||||||||
Sample |
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Keywords | 80S / ribosome / B-cells / EBV / epstein barr / M81 | |||||||||
| Function / homology | Function and homology informationtranslation at presynapse / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair ...translation at presynapse / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / negative regulation of formation of translation preinitiation complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of ubiquitin-protein transferase activity / GAIT complex / positive regulation of DNA-templated transcription initiation / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / G1 to G0 transition / Enterobacterial factors antagonize host defense / PD-L1(CD274) glycosylation and translocation to plasma membrane / erythrocyte homeostasis / supercoiled DNA binding / oxidized purine DNA binding / NF-kappaB complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / negative regulation of myoblast fusion / protein kinase A binding / Ribosomal scanning and start codon recognition / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / male meiosis I / Translation initiation complex formation / Dengue Virus Genome Translation and Replication / Maturation of DENV proteins / fibroblast growth factor binding / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / monocyte chemotaxis / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / cellular response to ethanol / Dengue Virus Attachment and Entry / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein targeting / negative regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / protein localization to nucleus / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / embryo implantation / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / regulation of translational fidelity / positive regulation of microtubule polymerization / SPOP-mediated proteasomal degradation of PD-L1(CD274) / maturation of LSU-rRNA / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / spindle assembly / Protein methylation / 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) / Nuclear events stimulated by ALK signaling in cancer / rough endoplasmic reticulum / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / mRNA Polyadenylation / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / laminin binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / negative regulation of protein ubiquitination / positive regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / Maturation of protein E / MDM2/MDM4 family protein binding / liver regeneration Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Fedorenko A / Bashan A / Yonath A | |||||||||
| Funding support | 1 items
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Citation | Journal: To Be PublishedTitle: An Epstein-Barr virus-encoded snoRNA directs 2-O-methylation of human rRNAs to control translation and the viral lytic switch Authors: Yarden D / Beata EJ | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_56227.map.gz | 65.2 MB | EMDB map data format | |
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| Header (meta data) | emd-56227-v30.xml emd-56227.xml | 99.3 KB 99.3 KB | Display Display | EMDB header |
| Images | emd_56227.png | 53.1 KB | ||
| Filedesc metadata | emd-56227.cif.gz | 20.5 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-56227 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-56227 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9tt7MC ![]() 9tv2C C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_56227.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Composite map of 80S ribosomes from primary B-cells infected with WT M81 Epstein-Barr virus. | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : 80S ribosome of primary B-cells infected with WT EBV M81
+Supramolecule #1: 80S ribosome of primary B-cells infected with WT EBV M81
+Macromolecule #1: 28S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #42: 18S rRNA
+Macromolecule #76: E-site tRNA
+Macromolecule #4: 60S ribosomal protein L4
+Macromolecule #5: 60S ribosomal protein L5
+Macromolecule #6: Large ribosomal subunit protein eL6
+Macromolecule #7: Large ribosomal subunit protein uL30
+Macromolecule #8: 60S ribosomal protein L7a
+Macromolecule #9: Large ribosomal subunit protein uL5
+Macromolecule #10: 60S ribosomal protein L14
+Macromolecule #11: 60S ribosomal protein L15
+Macromolecule #12: 60S ribosomal protein L13a
+Macromolecule #13: 60S ribosomal protein L17
+Macromolecule #14: 60S ribosomal protein L18
+Macromolecule #15: 60S ribosomal protein L21
+Macromolecule #16: 60S ribosomal protein L22
+Macromolecule #17: 60S ribosomal protein L23a
+Macromolecule #18: 60S ribosomal protein L26
+Macromolecule #19: 60S ribosomal protein L27
+Macromolecule #20: Large ribosomal subunit protein uL15
+Macromolecule #21: 60S ribosomal protein L29
+Macromolecule #22: 60S ribosomal protein L30
+Macromolecule #23: 60S ribosomal protein L31
+Macromolecule #24: 60S ribosomal protein L32
+Macromolecule #25: Large ribosomal subunit protein eL33
+Macromolecule #26: 60S ribosomal protein L34
+Macromolecule #27: 60S ribosomal protein L35
+Macromolecule #28: 60S ribosomal protein L36
+Macromolecule #29: Large ribosomal subunit protein eL37
+Macromolecule #30: 60S ribosomal protein L38
+Macromolecule #31: 60S ribosomal protein L39
+Macromolecule #32: Ubiquitin-60S ribosomal protein L40
+Macromolecule #33: 60S ribosomal protein L36a
+Macromolecule #34: 60S ribosomal protein L37a
+Macromolecule #35: 60S ribosomal protein L28
+Macromolecule #36: 60S ribosomal protein L8
+Macromolecule #37: Large ribosomal subunit protein uL3
+Macromolecule #38: 60S ribosomal protein L9
+Macromolecule #39: 60S ribosomal protein L10-like
+Macromolecule #40: Large ribosomal subunit protein eL13
+Macromolecule #41: 60S ribosomal protein L18a
+Macromolecule #43: 40S ribosomal protein SA
+Macromolecule #44: 40S ribosomal protein S3a
+Macromolecule #45: 40S ribosomal protein S2
+Macromolecule #46: 40S ribosomal protein S3
+Macromolecule #47: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #48: 40S ribosomal protein S5
+Macromolecule #49: 40S ribosomal protein S6
+Macromolecule #50: 40S ribosomal protein S7
+Macromolecule #51: 40S ribosomal protein S8
+Macromolecule #52: 40S ribosomal protein S9
+Macromolecule #53: 40S ribosomal protein S10
+Macromolecule #54: Small ribosomal subunit protein uS17
+Macromolecule #55: 40S ribosomal protein S13
+Macromolecule #56: 40S ribosomal protein S14
+Macromolecule #57: 40S ribosomal protein S15
+Macromolecule #58: 40S ribosomal protein S16
+Macromolecule #59: 40S ribosomal protein S17
+Macromolecule #60: 40S ribosomal protein S18
+Macromolecule #61: Small ribosomal subunit protein eS19
+Macromolecule #62: 40S ribosomal protein S20
+Macromolecule #63: 40S ribosomal protein S21
+Macromolecule #64: 40S ribosomal protein S15a
+Macromolecule #65: 40S ribosomal protein S23
+Macromolecule #66: 40S ribosomal protein S24
+Macromolecule #67: Small ribosomal subunit protein eS25
+Macromolecule #68: 40S ribosomal protein S26
+Macromolecule #69: 40S ribosomal protein S27
+Macromolecule #70: 40S ribosomal protein S28
+Macromolecule #71: 40S ribosomal protein S29
+Macromolecule #72: FAU ubiquitin like and ribosomal protein S30 fusion
+Macromolecule #73: RS8_HUMAN Small ribosomal subunit protein eS8
+Macromolecule #74: 60S ribosomal protein L41
+Macromolecule #75: 60S ribosomal protein L19
+Macromolecule #77: 60S ribosomal protein L23
+Macromolecule #78: 60S ribosomal protein L24
+Macromolecule #79: MAGNESIUM ION
+Macromolecule #80: POTASSIUM ION
+Macromolecule #81: SODIUM ION
+Macromolecule #82: ZINC ION
+Macromolecule #83: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | cell |
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Sample preparation
| Buffer | pH: 7.5 |
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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6305 / Average exposure time: 15.8 sec. / Average electron dose: 37.2 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
| Sample stage | Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
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Y (Row.)
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Processing
FIELD EMISSION GUN
