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Yorodumi- EMDB-10761: Mammalian 48S late-stage translation initiation complex (LS48S+eI... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10761 | |||||||||
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Title | Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / regulation of translational fidelity / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / PML body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / cysteine-type deubiquitinase activity / mitochondrial inner membrane / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) / Rabbit (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Bochler A / Simonetti A / Guca E / Hashem Y | |||||||||
Funding support | European Union, France, 2 items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structural Insights into the Mammalian Late-Stage Initiation Complexes. Authors: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem / Abstract: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC. | |||||||||
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_10761.map.gz | 202.6 MB | EMDB map data format | |
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Header (meta data) | emd-10761-v30.xml emd-10761.xml | 68.3 KB 68.3 KB | Display Display | EMDB header |
Images | emd_10761.png | 186 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10761 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10761 | HTTPS FTP |
-Validation report
Summary document | emd_10761_validation.pdf.gz | 352.3 KB | Display | EMDB validaton report |
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Full document | emd_10761_full_validation.pdf.gz | 351.4 KB | Display | |
Data in XML | emd_10761_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10761 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10761 | HTTPS FTP |
-Related structure data
Related structure data | 6yamMC 6yalC 6yanC 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_10761.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : LS48S+eIF3 IC with beta-globin mRNA
+Supramolecule #1: LS48S+eIF3 IC with beta-globin mRNA
+Supramolecule #2: LS48S+eIF3 IC
+Supramolecule #3: beta-globin mRNA
+Macromolecule #1: initiator methionylated tRNA
+Macromolecule #34: 18S ribosomal RNA
+Macromolecule #41: beta-globin mRNA
+Macromolecule #2: 60s ribosomal protein l41
+Macromolecule #3: 40S ribosomal protein uS2
+Macromolecule #4: 40S ribosomal protein eS1
+Macromolecule #5: 40S ribosomal protein uS5
+Macromolecule #6: 40S ribosomal protein uS3
+Macromolecule #7: 40S ribosomal protein eS4
+Macromolecule #8: 40S ribosomal protein uS7
+Macromolecule #9: 40S ribosomal protein eS6
+Macromolecule #10: ribosomal protein eS7
+Macromolecule #11: 40S ribosomal protein eS8
+Macromolecule #12: 40S ribosomal protein uS4
+Macromolecule #13: 40S ribosomal protein eS10
+Macromolecule #14: 40S ribosomal protein uS17
+Macromolecule #15: 40S ribosomal protein eS12
+Macromolecule #16: ribosomal protein uS15
+Macromolecule #17: 40S ribosomal protein uS11
+Macromolecule #18: 40S ribosomal protein uS9
+Macromolecule #19: 40S ribosomal protein eS17
+Macromolecule #20: 40S ribosomal protein eS19
+Macromolecule #21: 40S ribosomal protein uS10
+Macromolecule #22: 40S ribosomal protein eS21
+Macromolecule #23: 40S ribosomal protein uS8
+Macromolecule #24: 40S ribosomal protein uS12
+Macromolecule #25: 40S ribosomal protein eS24
+Macromolecule #26: 40S ribosomal protein eS26
+Macromolecule #27: 40S ribosomal protein eS27
+Macromolecule #28: 40S ribosomal protein eS28
+Macromolecule #29: ribosomal protein uS14
+Macromolecule #30: ribosomal protein eS31
+Macromolecule #31: ribosomal protein RACK1
+Macromolecule #32: ribosomal protein eS25
+Macromolecule #33: 40S ribosomal protein eS30
+Macromolecule #35: eukaryotic translation initiation factor 2 subunit alpha
+Macromolecule #36: eukaryotic translation initiation factor 2 subunit gamma
+Macromolecule #37: eukaryotic translation initiation factor 1A
+Macromolecule #38: ATP-binding cassette sub-family E member 1 (ABCE1)
+Macromolecule #39: 40S ribosomal protein uS13
+Macromolecule #40: 40S ribosomal protein uS19
+Macromolecule #42: eukaryotic translation initiation factor 3 subunit d
+Macromolecule #43: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #44: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #45: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #46: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #47: eukaryotic translation initiation factor 3 subunit h
+Macromolecule #48: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #49: eukaryotic translation initiation factor 3 subunit l
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #51: IRON/SULFUR CLUSTER
+Macromolecule #52: MAGNESIUM ION
+Macromolecule #53: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43450 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6yam: |