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- EMDB-2166: Architecture of human translation initiation factor 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-2166
TitleArchitecture of human translation initiation factor 3
Map datacryo-EM reconstruction of the eIF3 PCI-MPN core complex
Sample
  • Sample: PCI MPN core of the human eukaryotic translation initiation factor eIF3
  • Protein or peptide: eIF3 a
  • Protein or peptide: eIF3 c
  • Protein or peptide: eIF3 e
  • Protein or peptide: eIF3 f
  • Protein or peptide: eIF3 h
  • Protein or peptide: eIF3 k
  • Protein or peptide: eIF3 l
  • Protein or peptide: eIF3 m
Keywordstranslation initiation / eukaryotic initiation factor 3 / ribosome / proteasome / PCI-MPN domains
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.0 Å
AuthorsQuerol-Audi J / Sun C / Vogan J / Cate J / Nogales E
CitationJournal: Structure / Year: 2013
Title: Architecture of human translation initiation factor 3.
Authors: Jordi Querol-Audi / Chaomin Sun / Jacob M Vogan / M Duane Smith / Yu Gu / Jamie H D Cate / Eva Nogales /
Abstract: Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron ...Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron microscopy, we reveal the molecular organization of ten human eIF3 subunits, including an octameric core. The structure of eIF3 bears a close resemblance to that of the proteasome lid, with a conserved spatial organization of eight core subunits containing PCI and MPN domains that coordinate functional interactions in both complexes. We further show that eIF3 subunits a and c interact with initiation factors eIF1 and eIF1A, which control the stringency of start codon selection. Finally, we find that subunit j, which modulates messenger RNA interactions with the small ribosomal subunit, makes multiple independent interactions with the eIF3 octameric core. These results highlight the conserved architecture of eIF3 and how it scaffolds key factors that control translation initiation in higher eukaryotes, including humans.
History
DepositionAug 1, 2012-
Header (metadata) releaseAug 15, 2012-
Map releaseMay 8, 2013-
UpdateMay 29, 2013-
Current statusMay 29, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2166.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM reconstruction of the eIF3 PCI-MPN core complex
Voxel sizeX=Y=Z: 2.31 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-5.28531122 - 14.033560749999999
Average (Standard dev.)0.00000038 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 332.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.312.312.31
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z332.640332.640332.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-5.28514.0340.000

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Supplemental data

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Sample components

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Entire : PCI MPN core of the human eukaryotic translation initiation facto...

EntireName: PCI MPN core of the human eukaryotic translation initiation factor eIF3
Components
  • Sample: PCI MPN core of the human eukaryotic translation initiation factor eIF3
  • Protein or peptide: eIF3 a
  • Protein or peptide: eIF3 c
  • Protein or peptide: eIF3 e
  • Protein or peptide: eIF3 f
  • Protein or peptide: eIF3 h
  • Protein or peptide: eIF3 k
  • Protein or peptide: eIF3 l
  • Protein or peptide: eIF3 m

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Supramolecule #1000: PCI MPN core of the human eukaryotic translation initiation facto...

SupramoleculeName: PCI MPN core of the human eukaryotic translation initiation factor eIF3
type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Subcomplex containing 8 core subunits / Number unique components: 8
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: eIF3 a

MacromoleculeName: eIF3 a / type: protein_or_peptide / ID: 1 / Details: truncated version, contains residues 5-654 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: n/atruncated version, contains residues 302-913
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: eIF3 c

MacromoleculeName: eIF3 c / type: protein_or_peptide / ID: 2 / Details: truncated version, contains residues 302-913 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #3: eIF3 e

MacromoleculeName: eIF3 e / type: protein_or_peptide / ID: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #4: eIF3 f

MacromoleculeName: eIF3 f / type: protein_or_peptide / ID: 4 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #5: eIF3 h

MacromoleculeName: eIF3 h / type: protein_or_peptide / ID: 5 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #6: eIF3 k

MacromoleculeName: eIF3 k / type: protein_or_peptide / ID: 6 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #7: eIF3 l

MacromoleculeName: eIF3 l / type: protein_or_peptide / ID: 7 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #8: eIF3 m

MacromoleculeName: eIF3 m / type: protein_or_peptide / ID: 8 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Details: 20mM Hepes, 75mM KCl, 0.5mM EDTA, 1mM DTT, 2mM MgCl2, 3% trehalose
StainingType: NEGATIVE / Details: vitrified
GridDetails: C-flat plasma cleaned with Solarus
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateOct 9, 2011
Image recordingNumber real images: 2100 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each image
Final two d classificationNumber classes: 4000
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 172533
Detailsautomatic particle selection with template correlator

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