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- PDB-6ybt: Structure of a human 48S translational initiation complex - eIF3bgi -

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Basic information

Entry
Database: PDB / ID: 6ybt
TitleStructure of a human 48S translational initiation complex - eIF3bgi
Components
  • Eukaryotic translation initiation factor 3 subunit A
  • Eukaryotic translation initiation factor 3 subunit B
  • Eukaryotic translation initiation factor 3 subunit I
KeywordsTRANSLATION / eIF3 / ribosome / initiation complex
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / regulation of translational initiation / translation initiation factor binding / molecular adaptor activity / translation initiation factor activity / translational initiation / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / microtubule / postsynaptic density / mRNA binding / synapse / nucleolus / structural molecule activity / RNA binding / extracellular exosome / membrane / nucleoplasm / cytosol / cytoplasm
Nucleotide-binding alpha-beta plait domain superfamily / Eukaryotic translation initiation factor 3 subunit B / WD40-repeat-containing domain superfamily / RNA-binding domain superfamily / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / WD40 repeat, conserved site / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily ...Nucleotide-binding alpha-beta plait domain superfamily / Eukaryotic translation initiation factor 3 subunit B / WD40-repeat-containing domain superfamily / RNA-binding domain superfamily / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / WD40 repeat, conserved site / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / RNA recognition motif domain / Translation initiation factor, beta propellor-like domain / Proteasome component (PCI) domain / WD40 repeat
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsBrito Querido, J. / Sokabe, M. / Kraatz, S. / Gordiyenko, Y. / Skehel, M. / Fraser, C. / Ramakrishnan, V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
u: Eukaryotic translation initiation factor 3 subunit A
2: Eukaryotic translation initiation factor 3 subunit I
1: Eukaryotic translation initiation factor 3 subunit B


Theoretical massNumber of molelcules
Total (without water)292,3173
Polymers292,3173
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


Mass: 163179.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14152
#2: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting ...eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting protein 1 / TRIP-1 / eIF-3-beta / eIF3 p36


Mass: 36543.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13347
#3: 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: 92593.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55884

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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: Eukaryotic translation initiation factor / Type: RIBOSOME / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy
Image recordingAverage exposure time: 1 sec. / Electron dose: 107 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144882 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 616.69 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00775444
ELECTRON MICROSCOPYf_angle_d1.68167543
ELECTRON MICROSCOPYf_chiral_restr0.0741000
ELECTRON MICROSCOPYf_plane_restr0.00881072
ELECTRON MICROSCOPYf_dihedral_angle_d13.90791029

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