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- EMDB-3057: Structure of mammalian eIF3 in the context of the 43S preinitiati... -

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Basic information

Entry
Database: EMDB / ID: EMD-3057
TitleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Map dataReconstruction of mammalian preinitiation complex after focused classification on the eIF3g/i/b peripheral subunits complex of eIF3
Sample
  • Sample: Mammalian 43S preinitiation complex bound to DHX29
  • Complex: 40S small ribosomal subunit
  • Protein or peptide: eukaryotic initiation factor 3
  • Protein or peptide: eukaryotic initiation factor 2
  • Protein or peptide: DHX29
  • Protein or peptide: eIF1
  • Protein or peptide: eIF1AEIF1AX
  • RNA: initiator transfer RNA
KeywordseIF3 / eIF3 octamer core / mammalian preinitiation 34S complex / eIF3g/i/b / eIF3d
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translational initiation / translation initiation factor activity / cytoplasmic stress granule / RNA binding
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit I / 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 ...Eukaryotic translation initiation factor 3 subunit I / 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 / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
Authorsdes-Georges A / Dhote V / Kuhn L / Hellen CUT / Pestova TV / Frank J / Hashem Y
CitationJournal: Nature / Year: 2015
Title: Structure of mammalian eIF3 in the context of the 43S preinitiation complex.
Authors: Amedee des Georges / Vidya Dhote / Lauriane Kuhn / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / Yaser Hashem /
Abstract: During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of ...During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of messenger RNA and scan along it to the initiation codon. Scanning on structured mRNAs also requires the DExH-box protein DHX29. Mammalian eIF3 contains 13 subunits and participates in nearly all steps of translation initiation. Eight subunits having PCI (proteasome, COP9 signalosome, eIF3) or MPN (Mpr1, Pad1, amino-terminal) domains constitute the structural core of eIF3, to which five peripheral subunits are flexibly linked. Here we present a cryo-electron microscopy structure of eIF3 in the context of the DHX29-bound 43S complex, showing the PCI/MPN core at ∼6 Å resolution. It reveals the organization of the individual subunits and their interactions with components of the 43S complex. We were able to build near-complete polyalanine-level models of the eIF3 PCI/MPN core and of two peripheral subunits. The implications for understanding mRNA ribosomal attachment and scanning are discussed.
History
DepositionJun 21, 2015-
Header (metadata) releaseAug 5, 2015-
Map releaseSep 9, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: PDBe / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-5a5u
  • Surface level: 0.05
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5a5u
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Structure viewerEM map:
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Supplemental images

EMD-3057_ima...

Downloads & links

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Map

FileDownload / File: emd_3057.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mammalian preinitiation complex after focused classification on the eIF3g/i/b peripheral subunits complex of eIF3
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.26261827 - 0.40436754
Average (Standard dev.)0.00070926 (±0.01986324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z498.000498.000498.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2630.4040.001

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Supplemental data

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Sample components

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Entire : Mammalian 43S preinitiation complex bound to DHX29

EntireName: Mammalian 43S preinitiation complex bound to DHX29
Components
  • Sample: Mammalian 43S preinitiation complex bound to DHX29
  • Complex: 40S small ribosomal subunit
  • Protein or peptide: eukaryotic initiation factor 3
  • Protein or peptide: eukaryotic initiation factor 2
  • Protein or peptide: DHX29
  • Protein or peptide: eIF1
  • Protein or peptide: eIF1AEIF1AX
  • RNA: initiator transfer RNA

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Supramolecule #1000: Mammalian 43S preinitiation complex bound to DHX29

SupramoleculeName: Mammalian 43S preinitiation complex bound to DHX29 / type: sample / ID: 1000 / Number unique components: 7

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Supramolecule #1: 40S small ribosomal subunit

SupramoleculeName: 40S small ribosomal subunit / type: complex / ID: 1 / Name.synonym: SSU / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: Cytoplasm

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Macromolecule #1: eukaryotic initiation factor 3

MacromoleculeName: eukaryotic initiation factor 3 / type: protein_or_peptide / ID: 1 / Name.synonym: eIF3 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm

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Macromolecule #2: eukaryotic initiation factor 2

MacromoleculeName: eukaryotic initiation factor 2 / type: protein_or_peptide / ID: 2 / Name.synonym: eIF2 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm

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Macromolecule #3: DHX29

MacromoleculeName: DHX29 / type: protein_or_peptide / ID: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQ31

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Macromolecule #4: eIF1

MacromoleculeName: eIF1 / type: protein_or_peptide / ID: 4 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQ31

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Macromolecule #5: eIF1A

MacromoleculeName: eIF1A / type: protein_or_peptide / ID: 5 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Blood / Cell: Reticulcytes / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQ31

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Macromolecule #6: initiator transfer RNA

MacromoleculeName: initiator transfer RNA / type: rna / ID: 6 / Name.synonym: tRNAiMet / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: 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

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30120 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: GATAN HELIUM
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
DateNov 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 6.35 µm / Average electron dose: 25 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 54410

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