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Yorodumi- EMDB-72171: Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA... -
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Basic information
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| Title | Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORF | |||||||||||||||
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Keywords | Ribosome / IRES / Translation / Initiation | |||||||||||||||
| Function / homology | Function and homology informationguanyl nucleotide binding / kinase activator activity / 90S preribosome / ubiquitin ligase inhibitor activity / translation elongation factor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / translation regulator activity / rough endoplasmic reticulum ...guanyl nucleotide binding / kinase activator activity / 90S preribosome / ubiquitin ligase inhibitor activity / translation elongation factor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / gastrulation / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to epidermal growth factor stimulus / cytosolic ribosome / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA / small-subunit processome / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / regulation of translation / rhythmic process / positive regulation of canonical Wnt signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / killing of cells of another organism / cytosolic large ribosomal subunit / defense response to Gram-negative bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / perikaryon / cell differentiation / cytoplasmic translation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / GTPase activity / apoptotic process / centrosome / synapse / dendrite / GTP binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
| Biological species | ![]() Nedicistrovirus TFN-2012 | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | De S / Altomare CG / Abaeva IS / Dadhwal P / Garg P / Acosta-Reyes F / Brown ZP / Pestova TV / Hellen CUT / Frank J | |||||||||||||||
| Funding support | United States, 4 items
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Citation | Journal: Nucleic Acids Res / Year: 2026Title: Structural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation. Authors: Swastik De / Clara G Altomare / Irina S Abaeva / Prikshat Dadhwal / Priyanka Garg / Francisco Acosta-Reyes / Zuben P Brown / Tatyana V Pestova / Christopher U T Hellen / Joachim Frank / ![]() Abstract: We utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high- ...We utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high-resolution structures of 80S ribosome complexes with the NediV IRES in various functional states, including binary complexes, aminoacyl-transfer RNA (tRNA)-bound complexes, and complexes with elongation factor eEF2. In binary complexes, the NediV IRES primarily occupies the ribosomal P site, exhibiting conformational flexibility and engaging the ribosome at multiple interaction sites. Upon translocation, the IRES undergoes structural rearrangements, including destabilization of its PKI domain, facilitating the transition to canonical elongation. Crucially, we captured an eEF2-bound complex, along with an eEF1A-bound failed decoding complex featuring a mismatched tRNA, the latter representing the first instance of a canonical elongation complex visualized in the presence of a natural, hydrolysable nucleotide and without the addition of any trapping agents. These findings provide a comprehensive structural overview of IGR IRES-mediated translation initiation and its transition to elongation, revealing key mechanistic details of viral translation and proofreading. | |||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_72171.map.gz | 259 MB | EMDB map data format | |
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| Header (meta data) | emd-72171-v30.xml emd-72171.xml | 109.8 KB 109.8 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_72171_fsc_1.xml emd_72171_fsc_2.xml | 16.8 KB 16.8 KB | Display Display | FSC data file |
| Images | emd_72171.png | 85.6 KB | ||
| Filedesc metadata | emd-72171.cif.gz | 19.9 KB | ||
| Others | emd_72171_additional_1.map.gz emd_72171_half_map_1.map.gz emd_72171_half_map_2.map.gz | 482 MB 475.4 MB 475.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-72171 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-72171 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9q2pMC ![]() 9q1qC ![]() 9q1sC ![]() 9q2mC ![]() 9q2tC M: atomic model generated by this map C: citing same article ( |
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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_72171.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.66 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: #1
| File | emd_72171_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_72171_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_72171_half_map_2.map | ||||||||||||
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Sample components
+Entire : NediV IRES (P-site) in complex with Rabbit 80S
+Supramolecule #1: NediV IRES (P-site) in complex with Rabbit 80S
+Macromolecule #1: 5S ribosomal RNA
+Macromolecule #46: tRNA
+Macromolecule #47: 28S ribosomal RNA
+Macromolecule #48: 5.8S ribosomal RNA
+Macromolecule #49: 18S ribosomal RNA
+Macromolecule #83: A*/T tRNA
+Macromolecule #85: NediV ORF
+Macromolecule #2: 60S ribosomal protein L8
+Macromolecule #3: 60S ribosomal protein L3
+Macromolecule #4: 60S ribosomal protein L4
+Macromolecule #5: 60S ribosomal protein L5
+Macromolecule #6: 60S ribosomal protein L6
+Macromolecule #7: 60S ribosomal protein L7
+Macromolecule #8: Large ribosomal subunit protein eL8
+Macromolecule #9: 60S ribosomal protein L9
+Macromolecule #10: Ribosomal protein L10
+Macromolecule #11: 60S ribosomal protein L11
+Macromolecule #12: Large ribosomal subunit protein eL13
+Macromolecule #13: 60S ribosomal protein L14
+Macromolecule #14: 60S ribosomal protein L15
+Macromolecule #15: Large ribosomal subunit protein uL13
+Macromolecule #16: 60S ribosomal protein L17
+Macromolecule #17: Large ribosomal subunit protein eL18
+Macromolecule #18: 60S ribosomal protein L19
+Macromolecule #19: 60S ribosomal protein L18a
+Macromolecule #20: 60S ribosomal protein L21
+Macromolecule #21: Large ribosomal subunit protein eL22
+Macromolecule #22: Large ribosomal subunit protein uL14
+Macromolecule #23: uL24
+Macromolecule #24: Large ribosomal subunit protein uL23
+Macromolecule #25: 60S ribosomal protein L26
+Macromolecule #26: 60S ribosomal protein L27
+Macromolecule #27: 60S ribosomal protein L27a
+Macromolecule #28: eL29
+Macromolecule #29: 60S ribosomal protein L30
+Macromolecule #30: 60S ribosomal protein L31
+Macromolecule #31: Large ribosomal subunit protein eL32
+Macromolecule #32: Large ribosomal subunit protein eL33
+Macromolecule #33: 60S ribosomal protein L34
+Macromolecule #34: 60S ribosomal protein L35
+Macromolecule #35: 60S ribosomal protein L36
+Macromolecule #36: 60S ribosomal protein L37
+Macromolecule #37: Large ribosomal subunit protein eL38
+Macromolecule #38: 60S ribosomal protein L39
+Macromolecule #39: Large ribosomal subunit protein eL40
+Macromolecule #40: eL41
+Macromolecule #41: eL42
+Macromolecule #42: 60S ribosomal protein L37a
+Macromolecule #43: 60S ribosomal protein L28
+Macromolecule #44: 60S acidic ribosomal protein P0
+Macromolecule #45: uL11
+Macromolecule #50: 40S_SA_C domain-containing protein
+Macromolecule #51: 40S ribosomal protein S3a
+Macromolecule #52: 40S ribosomal protein S2
+Macromolecule #53: 40S ribosomal protein S3
+Macromolecule #54: 40S ribosomal protein S4
+Macromolecule #55: Small ribosomal subunit protein uS7
+Macromolecule #56: 40S ribosomal protein S6
+Macromolecule #57: Small ribosomal subunit protein eS7
+Macromolecule #58: 40S ribosomal protein S8
+Macromolecule #59: 40S ribosomal protein S9
+Macromolecule #60: 40S ribosomal protein S10
+Macromolecule #61: Small ribosomal subunit protein uS17
+Macromolecule #62: 40S ribosomal protein S12
+Macromolecule #63: 40S ribosomal protein S13
+Macromolecule #64: Small ribosomal subunit protein uS11
+Macromolecule #65: Small ribosomal subunit protein uS19
+Macromolecule #66: Small ribosomal subunit protein uS9
+Macromolecule #67: 40S ribosomal protein S17
+Macromolecule #68: 40S ribosomal protein S18
+Macromolecule #69: Small ribosomal subunit protein eS19
+Macromolecule #70: 40S ribosomal protein S20
+Macromolecule #71: eS21
+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: eS26
+Macromolecule #77: 40S ribosomal protein S27
+Macromolecule #78: 40S ribosomal protein S28
+Macromolecule #79: 40S ribosomal protein S29
+Macromolecule #80: Small ribosomal subunit protein eS30
+Macromolecule #81: 40S ribosomal protein S27a
+Macromolecule #82: Receptor of activated protein C kinase 1
+Macromolecule #84: Elongation factor 1-alpha 1
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ZINC ION
+Macromolecule #88: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI POLARA 300 |
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| Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 58.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Nedicistrovirus TFN-2012
Authors
United States, 4 items
Citation





















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Processing
FIELD EMISSION GUN


