Journal: 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
Deposition
Jun 21, 2015
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Header (metadata) release
Jul 8, 2015
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Map release
Sep 9, 2015
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Update
Oct 7, 2015
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Current status
Oct 7, 2015
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_3056.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Reconstruction of eIF3 octamer core
Voxel size
X=Y=Z: 1.66 Å
Density
Contour Level
By AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum
-0.06188392 - 0.12141231
Average (Standard dev.)
0.00010273 (±0.00224358)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
300
300
300
Spacing
300
300
300
Cell
A=B=C: 498.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.66
1.66
1.66
M x/y/z
300
300
300
origin x/y/z
0.000
0.000
0.000
length x/y/z
498.000
498.000
498.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-80
0
-4
NX/NY/NZ
161
13
58
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
300
300
300
D min/max/mean
-0.062
0.121
0.000
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Supplemental data
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Sample components
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Entire : eIF3 octamer core of Rabbit eIF3
Entire
Name: eIF3 octamer core of Rabbit eIF3
Components
Sample: eIF3 octamer core of Rabbit eIF3
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: eukaryotic initiation factor 1
Protein or peptide: eukaryotic initiation factor 1A
RNA: initiator transfer RNA
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Supramolecule #1000: eIF3 octamer core of Rabbit eIF3
Supramolecule
Name: eIF3 octamer core of Rabbit eIF3 / type: sample / ID: 1000 Details: The sample was monodisperse, eIF3 octamer core was locally refined from a reconstruction of the mammalian 43S preinitiation complex Oligomeric state: One octamer / Number unique components: 7
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI POLARA 300
Temperature
Min: 80 K / Max: 105 K / Average: 100 K
Date
Nov 1, 2013
Image recording
Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 6.35 µm / Number real images: 8000 / Average electron dose: 25 e/Å2
Tilt angle min
0
Tilt angle max
0
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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