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

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1976
Title	Functional reconstitution of the 13-subunit human translation initiation factor eIF3.
Map	3d reconstruction of 12mer human translation initiation factor eIF3
Sample	12mer of the human eukaryotic translation initiation factor eIF3
Keywords	translation initiation, eukaryotic initiation factor 3, ribosome, hepatitis C virus, internal ribosome entry site, proteasome, COP9 signalosome
Authors	Querol-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
Date	Deposition: 2011-10-08, Header release: 2011-11-03, Map release: 2011-12-21, Last update: 2011-12-21
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 4.8, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 4.8, Made by UCSF CHIMERA
Supplemental images	12mer_emd197...
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1975 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-2175 EMDB-2174 EMDB-2166 EMDB-2173 EMDB-2199 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 51, Page 20473-8, Year 2011
Title	Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3).
Authors	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 California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
Keywords	COP9 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)
Links	DOI: 10.1073/pnas.1116821108, PubMed: 22135459, PMC: PMC3251073

Map

File

EMD-1976.map ( map file in CCP4 format, 3540 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

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 Type

Image stored as Reals

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	96	96	96
Origin :	0	0	0
Limit :	95	95	95
Spacing :	96	96	96

Unit Cell

A = 418.56 A , B = 418.56 A , C = 418.56 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 4.36 A , Y = 4.36 A , Z = 4.36 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	4.36	4.36	4.36
M x/y/z	96	96	96
origin x/y/z	0.000	0.000	0.000
length x/y/z	418.560	418.560	418.560
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-56	-56	-55
NX/NY/NZ	112	112	112
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	96	96	96
start NC,NX/NR,NY/NS,NZ	0	0	0
NC,NX/NR,NY/NS,NZ	96	96	96
D min/max/mean	-5.177	15.962	0.000

Annotation Details

3d reconstruction of 12mer human translation initiation factor eIF3

Supplement
Images
Images	12mer_emd197...

Sample
Name	12mer of the human eukaryotic translation initiation factor eIF3
Number of Components	1
Oligomeric State	Subcomplex containing 12 subunits, missing j subunit
Theoretical Mass	0.7 MDa
Details	The sample was monodisperse
Component #1: cellular-component - eIF3 a
Scientific name	eIF3 a
Details	truncated version, contains residues 5-654
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #2: cellular-component - eIF3 b
Scientific name	eIF3 b
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #3: cellular-component - eIF3 c
Scientific name	eIF3 c
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Details	truncated version, contains residues 302-913
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #4: cellular-component - eIF3 d
Scientific name	eIF3 d
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #5: cellular-component - eIF3 e
Scientific name	eIF3 e
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #6: cellular-component - eIF3 f
Scientific name	eIF3 f
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #7: cellular-component - eIF3 g
Scientific name	eIF3 g
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #8: cellular-component - eIF3 h
Scientific name	eIF3 h
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #9: cellular-component - eIF3 i
Scientific name	eIF3 i
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #10: cellular-component - eIF3 k
Scientific name	eIF3 k
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #11: cellular-component - eIF3 l
Scientific name	eIF3 l
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Component #12: cellular-component - eIF3 m
Scientific name	eIF3 m
Theoretical Mass	0.7 MDa
Experimental Mass	0.7 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Natural Source	Cell Location: Cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)

Experiment
Sample Preparation
Staining	Grids with adsorbed protein stained with 3% w/v uranyl acetate for 40 seconds.
Specimen Conc	0.02 mg/ml
Specimen Support Details	200 mesh Cu grid
Specimen State	particle
Buffer	Details: 20 mM HEPES, 120 mM KCl, 1 mM DTT, 1 mM EDTA, 1 mM EGTA, 3% trehalose pH: 7.5
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI 12
Electron Gun
Electron Source	LAB6
Accelerating Voltage	120 kV
Electron Dose	20 e/A**2
Illumination Mode	SPOT SCAN
Lens
Magnification	Nominal: 49000 X,
Astigmatism	objective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs	6.3 mm
Imaging Mode	BRIGHT FIELD
Defocus	600 nm - 1500 nm
Specimen Holder
Holder	Eucentric ( SIDE ENTRY, EUCENTRIC )
Camera
Detector	TVIPS 4kx4k
Image Acquisition
Number of Digital Images	340
Details	Data collected using TVIPS camera

Processing
Method	single particle reconstruction
3 D reconstruction
Euler Angles Details	EMAN2 with initial and final angular steps of 25 and 10 degrees
Software	EMAN2
CTF Correction	Whole image
Resolution By Author	29.3
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Class Averages	400
Number of Projections	12457
Details	The particles were selected using an automatic selection program.

Download

Data from EMDB

Header (meta data in XML format)

emd-1976.xml (18.7 KB)

Map data

emd_1976.map.gz (2.5 MB)

Images

12mer_emd1976.jpg (21 KB)

FTP directory

ftp://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