+
Open data
-
Basic information
| Entry | ![]() | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
| |||||||||
Keywords | 80S / ribosome / B-cells / EBV / epstein barr / M81 | |||||||||
| Function / homology | Function and homology informationmale meiosis I / translation at presynapse / response to insecticide / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...male meiosis I / translation at presynapse / response to insecticide / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / G1 to G0 transition / negative regulation of formation of translation preinitiation complex / nucleolus organization / positive regulation of ubiquitin-protein transferase activity / positive regulation of DNA-templated transcription initiation / negative regulation of RNA splicing / GAIT complex / negative regulation of DNA repair / TORC2 complex binding / erythrocyte homeostasis / supercoiled DNA binding / rRNA modification in the nucleus and cytosol / oxidized purine DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / cytoplasmic translational initiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of translation involved in cellular response to UV / A band / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to aldosterone / negative regulation of myoblast fusion / protein-DNA complex disassembly / Ribosomal scanning and start codon recognition / protein kinase A binding / Translation initiation complex formation / positive regulation of DNA damage response, signal transduction by p53 class mediator / fibroblast growth factor binding / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / monocyte chemotaxis / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / SARS-CoV-1 modulates host translation machinery / protein localization to nucleus / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein targeting / Eukaryotic Translation Termination / Dengue Virus Attachment and Entry / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / positive regulation of microtubule polymerization / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / Protein methylation / positive regulation of cell cycle / 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal small subunit export from nucleus / negative regulation of protein ubiquitination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / rough endoplasmic reticulum / laminin binding / positive regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / MDM2/MDM4 family protein binding / Maturation of protein E / Mitotic Prometaphase / ER Quality Control Compartment (ERQC) / translation initiation factor binding / EML4 and NUDC in mitotic spindle formation / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex 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
| |||||||||
Citation | Journal: Cell Rep / Year: 2026Title: An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch. Authors: Yarden Dan / Beáta E Jády / Yudit Halperin / Yuval Nevo / Aliza Fedorenko / Anat Bashan / Maram Arafat / Pnina Glick / Ada Yonath / Tamás Kiss / Daphna Nachmani / ![]() Abstract: Epstein-Barr virus (EBV) establishes life-long latency in human B cells yet the molecular strategies that balance its persistence with lytic replication remain incompletely understood. Here, we ...Epstein-Barr virus (EBV) establishes life-long latency in human B cells yet the molecular strategies that balance its persistence with lytic replication remain incompletely understood. Here, we identify the EBV-encoded small nucleolar RNA, v-snoRNA1, as a bona fide 2'-O-methylation guide that directs methylation of host ribosomal RNAs at 18S-C621 and 28S-U1760, two conserved residues in the ribosomal A-site. V-snoRNA1-mediated hypermethylation impairs 18S rRNA maturation and compromises translational fidelity and output, resulting in slower cellular proliferation. Infection with a v-snoRNA1 deleted virus (Δv-snoRNA1) leads to enhanced protein synthesis and increased proliferation, together with extensive rewiring of host and viral gene expression. This rewiring includes suppression of immune and interferon pathways and alterations in transcription factor activities important for B cell differentiation. Importantly, we find that v-snoRNA1 is required to facilitate viral production. Our findings reveal a molecular strategy by which EBV directly controls translation to promote infection. | |||||||||
| History |
|
-
Structure visualization
| Supplemental images |
|---|
-
Downloads & links
-EMDB archive
| Map data | emd_56227.map.gz | 65.2 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-56227-v30.xml emd-56227.xml | 102.8 KB 102.8 KB | Display Display | EMDB header |
| Images | emd_56227.png | 53.1 KB | ||
| Filedesc metadata | emd-56227.cif.gz | 21 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-56227 ftp://data.pdbj.org/pub/emdb/structures/EMD-56227 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9tt7MC ![]() 9tv2C M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_56227.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
| ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
|
-Supplemental data
-
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 |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | cell |
-
Sample preparation
| Buffer | pH: 7.5 |
|---|---|
| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-
Electron microscopy
| Microscope | TFS KRIOS |
|---|---|
| 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 |
Movie
Controller
About Yorodumi




Keywords
Homo sapiens (human)
Authors
Citation









































Z (Sec.)
Y (Row.)
X (Col.)





















Processing
FIELD EMISSION GUN
