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Yorodumi- EMDB-26444: Mammalian 80S translation initiation complex with mRNA and Harrin... -
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Open data
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Basic information
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| Title | Mammalian 80S translation initiation complex with mRNA and Harringtonine | |||||||||
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Keywords | Mammalian / 80S / initiation / complex / mRNA modification / Harringtonine / RIBOSOME-INHIBITOR complex | |||||||||
| Function / homology | Function and homology informationregulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / ribosomal small subunit export from nucleus ...regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal large subunit biogenesis / DNA damage response, signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / cellular response to gamma radiation / spindle / mRNA 5'-UTR binding / transcription coactivator binding / rRNA processing / cytosolic ribosome / glucose homeostasis / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / perikaryon / cytoplasmic translation / postsynaptic density / protein stabilization / rRNA binding / mitochondrial inner membrane / structural constituent of ribosome / ribosome / translation / mRNA binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / nucleolus / dendrite / synapse / negative regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Yang R / Arango D / Sturgill D / Oberdoerffer S | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2022Title: Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Authors: Daniel Arango / David Sturgill / Renbin Yang / Tapan Kanai / Paulina Bauer / Jyoti Roy / Ziqiu Wang / Masaki Hosogane / Sarah Schiffers / Shalini Oberdoerffer / ![]() Abstract: mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent ...mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_26444.map.gz | 36.6 MB | EMDB map data format | |
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| Header (meta data) | emd-26444-v30.xml emd-26444.xml | 100.1 KB 100.1 KB | Display Display | EMDB header |
| Images | emd_26444.png | 71.9 KB | ||
| Filedesc metadata | emd-26444.cif.gz | 20.5 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-26444 ftp://data.pdbj.org/pub/emdb/structures/EMD-26444 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7ucjMC ![]() 7uckC 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_26444.map.gz / Format: CCP4 / Size: 421.9 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: 1.358 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 translation initiation complex with C(-1) mRNA and Harringtonine
+Supramolecule #1: 80S translation initiation complex with C(-1) mRNA and Harringtonine
+Macromolecule #1: P-site tRNA
+Macromolecule #2: mRNA
+Macromolecule #3: 28s rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #6: 18S rRNA
+Macromolecule #7: 60S ribosomal protein L8
+Macromolecule #8: 60S ribosomal protein L3
+Macromolecule #9: 60S ribosomal protein L4
+Macromolecule #10: Ribosomal_L18_c domain-containing protein
+Macromolecule #11: 60S ribosomal protein L6
+Macromolecule #12: 60S ribosomal protein L7
+Macromolecule #13: 60S ribosomal protein L7a
+Macromolecule #14: 60S ribosomal protein L9
+Macromolecule #15: Ribosomal protein L10
+Macromolecule #16: 60S ribosomal protein L11
+Macromolecule #17: 60S ribosomal protein L13
+Macromolecule #18: 60S ribosomal protein L14
+Macromolecule #19: 60S ribosomal protein L15
+Macromolecule #20: 60S ribosomal protein L13a
+Macromolecule #21: 60S ribosomal protein L17
+Macromolecule #22: 60S ribosomal protein L18
+Macromolecule #23: 60S ribosomal protein L19
+Macromolecule #24: 60S ribosomal protein L18a
+Macromolecule #25: 60S ribosomal protein L21
+Macromolecule #26: 60S ribosomal protein L22
+Macromolecule #27: 60S ribosomal protein L23
+Macromolecule #28: Ribosomal protein L24
+Macromolecule #29: 60S ribosomal protein L23a
+Macromolecule #30: 60S ribosomal protein L26
+Macromolecule #31: 60S ribosomal protein L27
+Macromolecule #32: 60S ribosomal protein L27a
+Macromolecule #33: 60S ribosomal protein L29
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L35a
+Macromolecule #38: 60S ribosomal protein L34
+Macromolecule #39: 60S ribosomal protein L35
+Macromolecule #40: 60S ribosomal protein L36
+Macromolecule #41: 60S ribosomal protein L37
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: 60S ribosomal protein L40
+Macromolecule #45: eL41
+Macromolecule #46: 60S ribosomal protein L36a
+Macromolecule #47: 60S ribosomal protein L37a
+Macromolecule #48: 60S ribosomal protein L28
+Macromolecule #49: 40S_SA_C domain-containing protein
+Macromolecule #50: 40S ribosomal protein S3a
+Macromolecule #51: 40S ribosomal protein S2
+Macromolecule #52: 40S ribosomal protein S3
+Macromolecule #53: 40S ribosomal protein S4
+Macromolecule #54: Ribosomal protein S5
+Macromolecule #55: 40S ribosomal protein S6
+Macromolecule #56: 40S ribosomal protein S7
+Macromolecule #57: 40S ribosomal protein S8
+Macromolecule #58: 40S ribosomal protein S9
+Macromolecule #59: 40S ribosomal protein S10
+Macromolecule #60: 40S ribosomal protein S11
+Macromolecule #61: 40S ribosomal protein S13
+Macromolecule #62: 40S ribosomal protein S14
+Macromolecule #63: 40S ribosomal protein S15
+Macromolecule #64: 40S ribosomal protein S16
+Macromolecule #65: 40S ribosomal protein S17
+Macromolecule #66: 40S ribosomal protein S18
+Macromolecule #67: 40S ribosomal protein S19
+Macromolecule #68: 40S ribosomal protein S20
+Macromolecule #69: eS21
+Macromolecule #70: 40S ribosomal protein S15a
+Macromolecule #71: 40S ribosomal protein S23
+Macromolecule #72: 40S ribosomal protein S24
+Macromolecule #73: 40S ribosomal protein S25
+Macromolecule #74: eS26
+Macromolecule #75: 40S ribosomal protein S27
+Macromolecule #76: 40S ribosomal protein S28
+Macromolecule #77: 40S ribosomal protein S29
+Macromolecule #78: 40S ribosomal protein S30
+Macromolecule #79: Receptor of activated protein C kinase 1
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: Harringtonine
+Macromolecule #82: ZINC ION
-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 TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Refinement | Space: REAL |
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| Output model | ![]() PDB-7ucj: |
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Keywords
Authors
United States, 1 items
Citation









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FIELD EMISSION GUN
