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- EMDB-10762: Mammalian 48S late-stage translation initiation complex with hist... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10762 | |||||||||
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Title | Mammalian 48S late-stage translation initiation complex with histone 4 mRNA | |||||||||
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Function / homology | ![]() eukaryotic translation initiation factor 2 complex / eukaryotic 48S preinitiation complex / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...eukaryotic translation initiation factor 2 complex / eukaryotic 48S preinitiation complex / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / 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 / small-subunit processome / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / modification-dependent protein catabolic process / spindle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / rRNA processing / G1/S transition of mitotic cell cycle / protein tag activity / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / glucose homeostasis / regulation of translation / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / mitochondrial inner membrane / 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 division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
![]() | Bochler A / Simonetti A / Guca E / Hashem Y | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 18.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 51.5 KB 51.5 KB | Display Display | ![]() |
Images | ![]() | 152.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yanMC ![]() 6yalC ![]() 6yamC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
+Entire : LS48S IC with histone 4 mRNA
+Supramolecule #1: LS48S IC with histone 4 mRNA
+Supramolecule #2: LS48S IC
+Supramolecule #3: histone 4 mRNA
+Macromolecule #1: 60s ribosomal protein l41
+Macromolecule #2: 40S ribosomal protein SA
+Macromolecule #3: ribosomal protein eS1
+Macromolecule #4: 40S ribosomal protein uS5
+Macromolecule #5: Ribosomal protein S3
+Macromolecule #6: 40S ribosomal protein S4
+Macromolecule #7: Ribosomal protein S5
+Macromolecule #8: 40S ribosomal protein S6
+Macromolecule #9: ribosomal protein eS7
+Macromolecule #10: 40S ribosomal protein S8
+Macromolecule #11: Ribosomal protein S9 (Predicted)
+Macromolecule #12: 40S ribosomal protein eS10
+Macromolecule #13: Ribosomal protein S11
+Macromolecule #14: 40S ribosomal protein S12
+Macromolecule #15: ribosomal protein uS15
+Macromolecule #16: 40S ribosomal protein uS11
+Macromolecule #17: ribosomal protein uS9
+Macromolecule #18: ribosomal protein eS17
+Macromolecule #19: 40S ribosomal protein eS19
+Macromolecule #20: Ribosomal_S10 domain-containing protein
+Macromolecule #21: 40S ribosomal protein S21
+Macromolecule #22: Ribosomal protein S15a
+Macromolecule #23: 40S ribosomal protein uS12
+Macromolecule #24: 40S ribosomal protein S24
+Macromolecule #25: 40S ribosomal protein eS26
+Macromolecule #26: 40S ribosomal protein S27
+Macromolecule #27: ribosomal protein eS28
+Macromolecule #28: ribosomal protein uS14
+Macromolecule #29: ribosomal protein eS31
+Macromolecule #30: ribosomal protein RACK1
+Macromolecule #31: ribosomal protein eS25
+Macromolecule #32: 40S ribosomal protein eS30
+Macromolecule #35: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #36: eukaryotic translation initiation factor 2 subunit gamma
+Macromolecule #37: 40S ribosomal protein uS13
+Macromolecule #38: Ribosomal protein S15
+Macromolecule #33: 18S ribosomal RNA
+Macromolecule #34: histone 4 (H4) mRNA
+Macromolecule #39: initiator methionylated tRNA
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372000 |
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-6yan: |