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- EMDB-10763: Mammalian late-stage translation initiation complex with beta-glo... -

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Basic information

Entry
Database: EMDB / ID: EMD-10763
TitleMammalian late-stage translation initiation complex with beta-globin mRNA in presence of ATP
Map data
Sample
  • Complex: LS48S IC + ATP with beta-globin mRNA
Function / homology
Function and homology information


ribosomal subunit / regulation of translational fidelity / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / ribosomal small subunit biogenesis / cytoplasmic stress granule / cytosolic small ribosomal subunit / cell differentiation / ribosome ...ribosomal subunit / regulation of translational fidelity / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / ribosomal small subunit biogenesis / cytoplasmic stress granule / cytosolic small ribosomal subunit / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / synapse / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / cytoplasm
Similarity search - Function
RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit ...RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 4Fe-4S binding domain / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S21e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Ribosomal protein S6/S6e/A/B/2, conserved site / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Plectin/S10 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / Ribosomal protein L30 signature. / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / Ribosomal protein S19 signature. / Ribosomal protein S7 signature. / Ribosomal protein S17 signature. / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S7p/S5e / S4 RNA-binding domain profile. / Ribosomal protein S11 signature. / Ubiquitin domain profile. / Ribosomal protein S9 signature. / Ribosomal protein S12 signature. / Ribosomal protein L23/L15e core domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / ATP binding cassette subfamily E member 1 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 ...Small ribosomal subunit protein eS32 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / ATP binding cassette subfamily E member 1 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS7 / Eukaryotic translation initiation factor 4C / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Ribosomal protein S5
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsSimonetti A / Guca E / Hashem Y
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)759120European Union
French National Research AgencyANR-14-ACHN-0024 France
CitationJournal: 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
DepositionMar 12, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateApr 22, 2020-
Current statusApr 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0697
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0697
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10763.png

Downloads & links

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Map

FileDownload / File: emd_10763.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.63 Å
Density
Contour LevelBy AUTHOR: 0.0697 / Movie #1: 0.0697
Minimum - Maximum-0.1599891 - 0.52191997
Average (Standard dev.)0.00054380327 (±0.03652955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 471.90002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.633.633.63
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z471.900471.900471.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-0.1600.5220.001

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Supplemental data

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Sample components

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Entire : LS48S IC + ATP with beta-globin mRNA

EntireName: LS48S IC + ATP with beta-globin mRNA
Components
  • Complex: LS48S IC + ATP with beta-globin mRNA

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Supramolecule #1: LS48S IC + ATP with beta-globin mRNA

SupramoleculeName: LS48S IC + ATP with beta-globin mRNA / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 26.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200000

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