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- EMDB-1976: Functional reconstitution of the 13-subunit human translation ini... -

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Entry
Database: EMDB / ID: 1976
TitleFunctional reconstitution of the 13-subunit human translation initiation factor eIF3.
Keywordstranslation initiation / eukaryotic initiation factor 3 / ribosome / hepatitis C virus / internal ribosome entry site / proteasome / COP9 signalosome
Sample12mer of the human eukaryotic translation initiation factor eIF3
SourceHomo sapiens / human
Map data3d reconstruction of 12mer human translation initiation factor eIF3
Methodsingle particle reconstruction, at 29.3 Å resolution
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
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 20473-20478

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 20473-20478 Yorodumi Papers
Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3).
Chaomin 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

DateDeposition: Oct 8, 2011 / Header (metadata) release: Nov 3, 2011 / Map release: Dec 21, 2011 / Last update: Dec 21, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 4.8
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1976.map.gz (map file in CCP4 format, 3457 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
4.36 Å/pix.
= 418.56 Å
96 pix
4.36 Å/pix.
= 418.56 Å
96 pix
4.36 Å/pix.
= 418.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.36 Å
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)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
CellA=B=C: 418.56 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-5.17715.9620.000

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Supplemental data

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Sample components

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Entire 12mer of the human eukaryotic translation initiation factor eIF3

EntireName: 12mer of the human eukaryotic translation initiation factor eIF3
Details: The sample was monodisperse / Number of components: 1
Oligomeric State: Subcomplex containing 12 subunits, missing j subunit
MassTheoretical: 700 kDa

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Component #1: cellular-component, eIF3 a

Cellular-componentName: eIF3 a / a.k.a: eIF3 a / Oligomeric Details: Monomer / Details: truncated version, contains residues 5-654 / Recombinant expression: Yes / Number of Copies: 1
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #2: cellular-component, eIF3 b

Cellular-componentName: eIF3 b / a.k.a: eIF3 b / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #3: cellular-component, eIF3 c

Cellular-componentName: eIF3 c / a.k.a: eIF3 c / Oligomeric Details: Monomer / Details: truncated version, contains residues 302-913 / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #4: cellular-component, eIF3 d

Cellular-componentName: eIF3 d / a.k.a: eIF3 d / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #5: cellular-component, eIF3 e

Cellular-componentName: eIF3 e / a.k.a: eIF3 e / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #6: cellular-component, eIF3 f

Cellular-componentName: eIF3 f / a.k.a: eIF3 f / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #7: cellular-component, eIF3 g

Cellular-componentName: eIF3 g / a.k.a: eIF3 g / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #8: cellular-component, eIF3 h

Cellular-componentName: eIF3 h / a.k.a: eIF3 h / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #9: cellular-component, eIF3 i

Cellular-componentName: eIF3 i / a.k.a: eIF3 i / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #10: cellular-component, eIF3 k

Cellular-componentName: eIF3 k / a.k.a: eIF3 k / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #11: cellular-component, eIF3 l

Cellular-componentName: eIF3 l / a.k.a: eIF3 l / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Component #12: cellular-component, eIF3 m

Cellular-componentName: eIF3 m / a.k.a: eIF3 m / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.02 mg/ml
Buffer solution: 20 mM HEPES, 120 mM KCl, 1 mM DTT, 1 mM EDTA, 1 mM EGTA, 3% trehalose
pH: 7.5
Support film200 mesh Cu grid
StainingGrids with adsorbed protein stained with 3% w/v uranyl acetate for 40 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 49000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 6.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 1500 nm
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: GENERIC TVIPS (4k x 4k)

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Image acquisition

Image acquisition
340
Image acquisition
Datacollec tedusingTV IPScamera

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 400 / Number of projections: 12457
Details: The particles were selected using an automatic selection program.
Applied symmetry: C1 (asymmetric)
3D reconstructionEuler angles: EMAN2 with initial and final angular steps of 25 and 10 degrees
Software: EMAN2 / CTF correction: Whole image / Resolution: 29.3 Å / Resolution method: FSC 0.5

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