EMDB-1327: Reconfiguration of yeast 40S ribosomal subunit domains...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1327
Authors	Gilbert RJC, Gordiyenko Y, von der Haar T, Sonnen AF-P, Hoffman GW, Nardelli M, Stuart DI, McCarthy JEG
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 22.408501399, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 22.408501399, Made by UCSF CHIMERA
Supplemental images	1327.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1328 Cite EMDB-1329 Cite EMDB-1330 Cite EMDB-1331 Cite EMDB-1332 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1331 EMDB-1329 EMDB-1330 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 14, Page 5788-93, Year 2007
Title	Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
Authors	Robert J C Gilbert, Yulya Gordiyenko, Tobias von der Haar, Andreas F-P Sonnen, Gregor Hofmann, Maria Nardelli, David I Stuart, John E G McCarthy Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
Keywords	5' Untranslated Regions, Codon, Initiator, Cryoelectron Microscopy, Eukaryotic Initiation Factor-1 (genetics), Eukaryotic Initiation Factor-2 (genetics), Eukaryotic Initiation Factor-3 (genetics), Eukaryotic Initiation Factor-5 (genetics), Models, Chemical, Models, Molecular, Protein Binding, Protein Biosynthesis, Protein Structure, Secondary, Protein Subunits, RNA, Fungal (genetics), RNA, Messenger (metabolism), Ribosomes (chemistry), Saccharomyces cerevisiae (genetics)
Links	DOI: 10.1073/pnas.0606880104, PubMed: 17389391, PMC: PMC1832216

Map

File

EMD-1327.map ( map file in CCP4 format, 8389 KB )

Projections & Slices

Size of images:

Axes	Y (Sec.)	X (Row.)	Z (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:	21.7, 22.4085014 (movie #1):
Minimum - Maximum:	-97.4 - 200
Average (Standard dev.):	1.93102 (13.2256)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	Z	X	Y
Dimensions :	128	128	128
Origin :	-64	-64	-64
Limit :	63	63	63
Spacing :	128	128	128

Unit Cell

A = 426.24 A , B = 426.24 A , C = 426.24 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 3.33 A , Y = 3.33 A , Z = 3.33 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	3.33	3.33	3.33
M x/y/z	128	128	128
origin x/y/z	0.000	0.000	0.000
length x/y/z	426.240	426.240	426.240
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-64	-64	-64
NX/NY/NZ	128	128	128
MAP C/R/S	3	1	2
start NC/NR/NS	-64	-64	-64
NC/NR/NS	128	128	128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-97.400	200.000	1.931

Annotation Details

Reconstruction of the 43S preinitiation complex from S. cerevisiae.

Supplement
Images
Images	1327.gif

Sample
Name	Eukaryotic translation preinitiation complex 43S
Oligomeric State	40S-Met-tRNA-eIF2-GMP-PNP-eIF3-eIF1-eIF1A
Number of Components	6
Theoretical Mass	1.941 MDa
Component #1: ribosome-eukaryote - 40S
Scientific name	Small subunit
Common Name	40S
Theoretical Mass	1.4 MDa
Experimental Mass	1.4 MDa
Details	S. cerevisiae
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	Baker's yeast
Eukaryote	SSU 40S
Recombinant expression	No
Component #2: nucleic-acid - tRNA
Scientific name	tRNA
Theoretical Mass	0.023 MDa
Experimental Mass	0.023 MDa
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	Baker's yeast
Synthetic	No
Structure	DOUBLE HELIX
Class	T-RNA
Component #3: protein - eIF2
Scientific name	eukaryotic translation initiation factor 2
Common Name	eIF2
Theoretical Mass	0.124 MDa
Experimental Mass	0.124 MDa
Oligomeric Details	heterotrimer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	Baker's yeast
Recombinant expression	Yes
Natural Source	Cell Location: Cytosol
Engineered Source	Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #4: protein - eIF3
Scientific name	eukaryotic translation initiation factor 3
Common Name	eIF3
Theoretical Mass	0.362 MDa
Experimental Mass	0.362 MDa
Oligomeric Details	Heteropentamer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	Baker's yeast
Recombinant expression	Yes
Natural Source	Cell Location: Cytosol
Engineered Source	Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #5: protein - eIF1
Scientific name	eukaryotic translation initiation factor 1
Common Name	eIF1
Theoretical Mass	0.012 MDa
Experimental Mass	0.012 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	Baker's yeast
Recombinant expression	Yes
Natural Source	Cell Location: Cytosol
Engineered Source	Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Component #6: protein - eIF1A
Scientific name	eukaryotic translation initiation factor 1A
Common Name	eIF1A
Theoretical Mass	0.017 MDa
Experimental Mass	0.017 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	Baker's yeast
Recombinant expression	Yes
Natural Source	Cell Location: Cytosol
Engineered Source	Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)

Experiment
Sample Preparation
Specimen Support Details	300 mesh copper grid with lacey carbon film
Specimen State	particle
Buffer	Details: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP pH: 7.4
Vitrification
Cryogen Name	ETHANE
Instrument	HOMEMADE PLUNGER
Method	Blot with Whatman number 1 paper for 1-2 seconds prior to plunging.
Details	Vitrification instrument: Home-made plunger
Imaging
Microscope	FEI/PHILIPS CM200FEG
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X,
Astigmatism	Astigmatism corrected at 100,000 x
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	2055 nm - 11685 nm
Specimen Holder
Holder	Eucentric ( GATAN LIQUID NITROGEN )
Temperature	100 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	70
Sampling Size	8.33 microns
Quant Bit Number	8
Scanner	OTHER

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Single particle
Software	IMAGIC, EMAN, FREALIGN, SPIDER, GAP
CTF Correction	Per micrograph
Resolution By Author	20.0
Resolution Method	FSC at 0.5 cut-off
Euler Angles Details	SPIDER Euler angle convention
Details	Final maps were computed from CTF-corrected (by phase flipping) images, and scaled in Fourier space to a scattering model of the structure.
Single Particle
Number of Projections	27101
Details	The particles were selected manually.
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Target Criteria	Real space CC and R-factor
Software	GAP
Refinement Space	REAL
Details	Protocol: Rigid body

Download

Data from EMDB

Header (meta data in XML format)

emd-1327.xml (12.5 KB)

Map data

emd_1327.map.gz (342.4 KB)

Images

1327.gif (53.8 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1327

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 5.2 MB Session file for UCSF-Chimera, 19.6 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.6 MB Session file for UCSF-Chimera, 19.9 KB