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- EMDB-1170: Structural roles for human translation factor eIF3 in initiation ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1170
TitleStructural roles for human translation factor eIF3 in initiation of protein synthesis.
Map dataCryo-EM density of human translation initiation factor eIF3.
Sample
  • Sample: Human eIF3Eukaryotic initiation factor 3
  • Protein or peptide: eIF3Eukaryotic initiation factor 3
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 33.0 Å
AuthorsSiridechadilok B / Fraser CS / Hall RJ / Doudna JA / Nogales E
CitationJournal: Science / Year: 2005
Title: Structural roles for human translation factor eIF3 in initiation of protein synthesis.
Authors: Bunpote Siridechadilok / Christopher S Fraser / Richard J Hall / Jennifer A Doudna / Eva Nogales /
Abstract: Protein synthesis in mammalian cells requires initiation factor eIF3, a approximately 750-kilodalton complex that controls assembly of 40S ribosomal subunits on messenger RNAs (mRNAs) bearing either ...Protein synthesis in mammalian cells requires initiation factor eIF3, a approximately 750-kilodalton complex that controls assembly of 40S ribosomal subunits on messenger RNAs (mRNAs) bearing either a 5'-cap or an internal ribosome entry site (IRES). Cryo-electron microscopy reconstructions show that eIF3, a five-lobed particle, interacts with the hepatitis C virus (HCV) IRES RNA and the 5'-cap binding complex eIF4F via the same domain. Detailed modeling of eIF3 and eIF4F onto the 40S ribosomal subunit reveals that eIF3 uses eIF4F or the HCV IRES in structurally similar ways to position the mRNA strand near the exit site of 40S, promoting initiation complex assembly.
History
DepositionOct 18, 2005-
Header (metadata) releaseOct 19, 2005-
Map releaseOct 19, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.140707752
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.140707752
  • 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_1170.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density of human translation initiation factor eIF3.
Voxel sizeX=Y=Z: 5.08 Å
Density
Contour Level1: 0.0185 / Movie #1: 0.1407078
Minimum - Maximum-0.45879 - 1.08984
Average (Standard dev.)0.000505202 (±0.0180367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 711.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.085.085.08
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z711.200711.200711.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-770
NX/NY/NZ15515578
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.4591.0900.001

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Supplemental data

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Sample components

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Entire : Human eIF3

EntireName: Human eIF3Eukaryotic initiation factor 3
Components
  • Sample: Human eIF3Eukaryotic initiation factor 3
  • Protein or peptide: eIF3Eukaryotic initiation factor 3

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Supramolecule #1000: Human eIF3

SupramoleculeName: Human eIF3 / type: sample / ID: 1000 / Details: human eIF3 purified from HeLa cytosol lysate. / Number unique components: 1
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: eIF3

MacromoleculeName: eIF3 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa / Organelle: Cytosol / Location in cell: Cytoplasm
Molecular weightExperimental: 750 KDa
Recombinant expressionOrganism: HeLa

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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

Concentration0.08 mg/mL
BufferpH: 7.5
Details: 20mM Tris pH7.5, 100mM KCl, 3mM MgCl2, 1mM DTT,0.1mM CHAPS, 2% Trehalose
StainingType: NEGATIVE / Details: cryo
GridDetails: holey-carbon with thin layer of carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: Phase flip
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC / Number images used: 12000

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