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- PDB-5k1h: eIF3b relocated to the intersubunit face to interact with eIF1 an... -

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Basic information

Entry
Database: PDB / ID: 5k1h
TitleeIF3b relocated to the intersubunit face to interact with eIF1 and below the eIF2 ternary-complex. from the structure of a partial yeast 48S preinitiation complex in closed conformation.
Components
  • Eukaryotic translation initiation factor 3 subunit B
  • eIF3a C-terminal tail
KeywordsTRANSLATION / eukaryotic translation initiation / ribosome / eIF3 peripheral subunits / cryo-EM
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / molecular adaptor activity / synapse / RNA binding / extracellular exosome / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsSimonetti, A. / Brito Querido, J. / Myasnikov, A.G. / Mancera-Martinez, E. / Renaud, A. / Kuhn, L. / Hashem, Y.
CitationJournal: Mol Cell / Year: 2016
Title: eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition.
Authors: Angelita Simonetti / Jailson Brito Querido / Alexander G Myasnikov / Eder Mancera-Martinez / Adeline Renaud / Lauriane Kuhn / Yaser Hashem /
Abstract: mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal ...mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 2.0Aug 9, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_end_seq_num / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_db_isoform / _struct_ref_seq.seq_align_end
Revision 2.1Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
B: Eukaryotic translation initiation factor 3 subunit B
A: eIF3a C-terminal tail


Theoretical massNumber of molelcules
Total (without water)71,5892
Polymers71,5892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / ...eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / eIF3 p110 / eIF3 p116


Mass: 66975.109 Da / Num. of mol.: 1 / Fragment: UNP Residues 170-745
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3B, EIF3S9 / Production host: Homo sapiens (human) / References: UniProt: P55884
#2: Protein eIF3a C-terminal tail


Mass: 4613.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of a partial yeast 48S preinitiation complex in closed conformation.
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 116 kDa/nm / Experimental value: NO
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
7VMDmodel fitting
13VMDmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254957 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Details: MDFF
Atomic model building

3D fitting-ID: 1 / Accession code: 5A5U / Initial refinement model-ID: 1 / PDB-ID: 5A5U

5a5u

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1B
2A

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