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- PDB-6ybv: Structure of a human 48S translational initiation complex - eIF2-TC -

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Basic information

Entry
Database: PDB / ID: 6ybv
TitleStructure of a human 48S translational initiation complex - eIF2-TC
Components
  • Eukaryotic translation initiation factor 2 subunit 1
  • Eukaryotic translation initiation factor 2 subunit 2
  • Eukaryotic translation initiation factor 2 subunit 3
  • Initiator methionine tRNA
  • mRNAMessenger RNA
KeywordsTRANSLATION / ribosome / initiation complex
Function / homology
Function and homology information


male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / positive regulation of type B pancreatic cell apoptotic process / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / translation factor activity, RNA binding ...male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / positive regulation of type B pancreatic cell apoptotic process / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / multi-eIF complex / translation factor activity, RNA binding / negative regulation of guanyl-nucleotide exchange factor activity / PERK-mediated unfolded protein response / protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / stress granule assembly / polysome / translation initiation factor binding / cellular response to amino acid starvation / response to endoplasmic reticulum stress / translation initiation factor activity / translational initiation / positive regulation of translational fidelity / cellular response to UV / cytoplasmic stress granule / positive regulation of neuron death / male gonad development / ribosome binding / cellular response to heat / transmembrane transport / cellular response to oxidative stress / in utero embryonic development / aging / cadherin binding / GTPase activity / protein autophosphorylation / mRNA binding / synapse / GTP binding / RNA binding / extracellular exosome / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Translation protein, beta-barrel domain superfamily / Translation elongation factor EFTu-like, domain 2 / P-loop containing nucleoside triphosphate hydrolase / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2, alpha subunit, middle domain superfamily / RNA-binding domain, S1 / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor 2, gamma subunit, C-terminal / Nucleic acid-binding, OB-fold ...Translation protein, beta-barrel domain superfamily / Translation elongation factor EFTu-like, domain 2 / P-loop containing nucleoside triphosphate hydrolase / Translation initiation factor 2, alpha subunit, C-terminal / Translation initiation factor 2, alpha subunit, middle domain superfamily / RNA-binding domain, S1 / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor 2, gamma subunit, C-terminal / Nucleic acid-binding, OB-fold / Translation initiation factor 2, alpha subunit / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Transcription factor, GTP-binding domain / Translation initiation factor IF2/IF5 / S1 domain
Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit 3 / gb:174924:
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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
s: Eukaryotic translation initiation factor 2 subunit 2
r: Eukaryotic translation initiation factor 2 subunit 1
w: Initiator methionine tRNA
k: mRNA
t: Eukaryotic translation initiation factor 2 subunit 3


Theoretical massNumber of molelcules
Total (without water)150,9685
Polymers150,9685
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 38454.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20042
#2: Protein Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 36161.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05198
#3: RNA chain Initiator methionine tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 174924
#4: RNA chain mRNA / Messenger RNA


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 51178.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41091, protein-synthesizing GTPase

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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: 48S initiation complex / Type: RIBOSOME / Entity ID: #1-#5 / 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
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33706 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 65.17 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00846970
ELECTRON MICROSCOPYf_angle_d1.45849840
ELECTRON MICROSCOPYf_chiral_restr0.07111235
ELECTRON MICROSCOPYf_plane_restr0.00871011
ELECTRON MICROSCOPYf_dihedral_angle_d25.30692598

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