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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 data
SampleMammalian 43S preinitiation complex bound to DHX29:
ribosome-eukaryote / (eukaryotic initiation factor ...) x 2 / DHX29 / eIF1 / eIF1AEIF1AX / nucleic-acidNucleic acid
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 / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation 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 / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / positive regulation of ATPase activity / regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA binding
Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Eukaryotic translation initiation factor 3 subunit B / WD40 repeat / RNA recognition motif domain / WD40/YVTN repeat-like-containing domain superfamily / Translation initiation factor, beta propellor-like domain / WD40-repeat-containing domain / Eukaryotic translation initiation factor 3 subunit I / eIF3B, RNA recognition motif ...Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Eukaryotic translation initiation factor 3 subunit B / WD40 repeat / RNA recognition motif domain / WD40/YVTN repeat-like-containing domain superfamily / Translation initiation factor, beta propellor-like domain / WD40-repeat-containing domain / Eukaryotic translation initiation factor 3 subunit I / eIF3B, RNA recognition motif / RNA-binding domain superfamily / WD40-repeat-containing domain superfamily
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 9 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.
Validation ReportSummary, Full report, XML, About validation report
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

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by height
  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 300 pix.
= 498. Å
1.66 Å/pix.
x 300 pix.
= 498. Å
1.66 Å/pix.
x 300 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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 / Number of components: 7

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Component #1: ribosome-eukaryote, 40S small ribosomal subunit

Ribosome-eukaryoteName: 40S small ribosomal subunit / a.k.a: SSU / Eukaryote: SSU 40S / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (natural)Location in cell: Cytoplasm / Cell: Reticulcytes / Organ or tissue: Blood

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Component #2: protein, eukaryotic initiation factor 3

ProteinName: eukaryotic initiation factor 3 / a.k.a: eIF3Eukaryotic initiation factor 3 / Oligomeric Details: Monomer / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (natural)Location in cell: cytoplasm / Cell: Reticulcytes / Organ or tissue: Blood

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Component #3: protein, eukaryotic initiation factor 2

ProteinName: eukaryotic initiation factor 2 / a.k.a: eIF2 / Oligomeric Details: Monomer / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (natural)Location in cell: cytoplasm / Cell: Reticulcytes / Organ or tissue: Blood

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Component #4: protein, DHX29

ProteinName: DHX29 / Oligomeric Details: Monomer / Recombinant expression: Yes
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pQ31
Source (natural)Location in cell: cytoplasm / Cell: Reticulcytes / Organ or tissue: Blood

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Component #5: protein, eIF1

ProteinName: eIF1 / Oligomeric Details: Monomer / Recombinant expression: Yes
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pQ31
Source (natural)Location in cell: cytoplasm / Cell: Reticulcytes / Organ or tissue: Blood

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Component #6: protein, eIF1A

ProteinName: eIF1AEIF1AX / Oligomeric Details: Monomer / Recombinant expression: Yes
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pQ31
Source (natural)Location in cell: cytoplasm / Cell: Reticulcytes / Organ or tissue: Blood

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Component #7: nucleic-acid, initiator transfer RNA

nucleic acidName: initiator transfer RNA / a.k.a: tRNAiMet / Class: T-RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Nov 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 30120 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4500 nm
Specimen HolderModel: GATAN HELIUM / Temperature: 100 (80 - 105 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 6.35 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 54410
3D reconstructionAlgorithm: Template matching / Software: Relion / CTF correction: Each particle / Resolution: 9 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Output model

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