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Functional reconstitution of the 13-subunit human translation initiation factor eIF3.

by single particle reconstruction, at 29.3 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 4.8, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 4.8, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1976
TitleFunctional reconstitution of the 13-subunit human translation initiation factor eIF3.
Map3d reconstruction of 12mer human translation initiation factor eIF3
Sample12mer of the human eukaryotic translation initiation factor eIF3
Keywordstranslation initiation, eukaryotic initiation factor 3, ribosome, hepatitis C virus, internal ribosome entry site, proteasome, COP9 signalosome
AuthorsQuerol-Audi J, Sun C, Todorovic A, Bai Y, Villa N, Snyder M, Ashchyan J, Lewis C, Hartland A, Gradia S, Fraser CS, Doudna JA, Nogales E, Cate JHD
DateDeposition: 2011-10-08, Header release: 2011-11-03, Map release: 2011-12-21, Last update: 2011-12-21
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 4.8, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 4.8, Image by UCSF CHIMERA

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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 51, Page 20473-8, Year 2011
TitleFunctional reconstitution of human eukaryotic translation initiation factor 3 (eIF3).
AuthorsChaomin Sun, Aleksandar Todorovic, Jordi Querol-Audí, Yun Bai, Nancy Villa, Monica Snyder, John Ashchyan, Christopher S Lewis, Abbey Hartland, Scott Gradia, Christopher S Fraser, Jennifer A Doudna, Eva Nogales, Jamie H D Cate
California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
KeywordsCOP9 signalosome complex, DNA, Complementary (metabolism), Escherichia coli (metabolism), Eukaryotic Initiation Factor-3 (chemistry), HeLa Cells, Hepacivirus (genetics), Humans, Microscopy, Electron (methods), Models, Molecular, Molecular Conformation, Multiprotein Complexes (chemistry), Peptide Hydrolases (chemistry, 3.4.-), Protein Binding, Protein Biosynthesis, Protein Structure, Tertiary, RNA, Messenger (metabolism), Ribosomes (chemistry)
LinksDOI: 10.1073/pnas.1116821108, PubMed: 22135459, PMC: PMC3251073
Map
Fileemd_1976.map.gz ( map file in CCP4 format, 3457 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
4.36 A/pix
= 418.56 A
96 pix
4.36 A/pix
= 418.56 A
96 pix
4.36 A/pix
= 418.56 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:4.8 (by author), 4.8 (movie #1):
Minimum - Maximum: -5.17689 - 15.9619
Average (Standard dev.): 1.55009e-09 (0.999999)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
Unit CellA= B= C: 418.56 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.36 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.364.364.36
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z418.560418.560418.560
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.17715.9620.000
Annotation Details3d reconstruction of 12mer human translation initiation factor eIF3
Supplement
Images
Images
Sample
Name12mer of the human eukaryotic translation initiation factor eIF3
Number of Components1
Oligomeric StateSubcomplex containing 12 subunits, missing j subunit
Theoretical Mass0.7MDa
DetailsThe sample was monodisperse
Component #1: cellular-component - eIF3 a
Scientific nameeIF3 a
Detailstruncated version, contains residues 5-654
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: cellular-component - eIF3 b
Scientific nameeIF3 b
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #3: cellular-component - eIF3 c
Scientific nameeIF3 c
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Detailstruncated version, contains residues 302-913
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #4: cellular-component - eIF3 d
Scientific nameeIF3 d
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #5: cellular-component - eIF3 e
Scientific nameeIF3 e
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #6: cellular-component - eIF3 f
Scientific nameeIF3 f
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #7: cellular-component - eIF3 g
Scientific nameeIF3 g
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #8: cellular-component - eIF3 h
Scientific nameeIF3 h
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #9: cellular-component - eIF3 i
Scientific nameeIF3 i
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #10: cellular-component - eIF3 k
Scientific nameeIF3 k
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #11: cellular-component - eIF3 l
Scientific nameeIF3 l
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #12: cellular-component - eIF3 m
Scientific nameeIF3 m
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
StainingGrids with adsorbed protein stained with 3% w/v uranyl acetate for 40 seconds.
Specimen Conc0.02 mg/ml
Specimen Support Details200 mesh Cu grid
Specimen Stateparticle
BufferDetails: 20 mM HEPES, 120 mM KCl, 1 mM DTT, 1 mM EDTA, 1 mM EGTA, 3% trehalose
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 49000
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs6.3 mm
Imaging ModeBRIGHT FIELD
Defocus600 nm - 1500 nm
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorGENERIC TVIPS (4k x 4k)
Image Acquisition
Number of Digital Images340
DetailsData collected using TVIPS camera
Processing
Methodsingle particle reconstruction
3D reconstruction
Euler Angles DetailsEMAN2 with initial and final angular steps of 25 and 10 degrees
SoftwareEMAN2
CTF CorrectionWhole image
Resolution By Author29.3 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages400
Number of Projections12457
DetailsThe particles were selected using an automatic selection program.
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1976.xml (18.7 KB)
Map dataemd_1976.map.gz (2.5 MB)
Images12mer_emd1976.jpg (21 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1976
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 27.9 KB