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Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates

by single particle reconstruction, at 22 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.15, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.15, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1925
TitleRibosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates
MapSurface rendered Rio2 depletion map
SampleS. cerevisiae pre-40S ribosomal particle depleted for Rio2
Keywordspre-40S, 40S intermediate, Rio2 depletion
AuthorsStrunk BS, Loucks CR, Su M, Vashisth H, Cheng S, Schilling J, BrooksIII CL, Karbstein K, Skiniotis G
DateDeposition: 2011-07-05, Header release: 2011-11-04, Map release: 2011-11-04, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.15, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.15, Made by UCSF CHIMERA

Supplemental images

1925.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

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Article
Citation - Primary
ArticleScience, Vol. 333, Issue 6048, Page 1449-53, Year 2011
TitleRibosome assembly factors prevent premature translation initiation by 40S assembly intermediates.
AuthorsBethany S Strunk, Cherisse R Loucks, Min Su, Harish Vashisth, Shanshan Cheng, Justin Schilling, Charles L Brooks, Katrin Karbstein, Georgios Skiniotis
Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA.
KeywordsBinding Sites, Cryoelectron Microscopy, DIM1 protein, S cerevisiae (2.1.1.-), Eukaryotic Initiation Factor-1 (chemistry), Eukaryotic Initiation Factor-3 (chemistry), Image Processing, Computer-Assisted, LTV1 protein, S cerevisiae, Methyltransferases (chemistry, 2.1.1.-), Models, Molecular, NOB1 protein, S cerevisiae, Nuclear Proteins (chemistry), Peptide Chain Initiation, Translational, Protein-Serine-Threonine Kinases (chemistry, 2.7.11.1), RNA, Fungal (genetics), RNA, Messenger (genetics), Ribosomal Proteins (chemistry), Ribosome Subunits, Small, Eukaryotic (chemistry), Rio2 protein, S cerevisiae (2.7.11.1), Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), eukaryotic peptide initiation factor-1A
LinksDOI: 10.1126/science.1208245, PubMed: 21835981, PMC: PMC3402165
Map
FileEMD-1925.map ( map file in CCP4 format, 16386 KB )
Projections & SlicesSize of images:
AxesZ (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:0.15 (by author), 0.15 (movie #1):
Minimum - Maximum: -1.10506451 - 1.87032986
Average (Standard dev.): 0.00177278 (0.18405762)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 160 160 160
Origin : 0 0 0
Limit : 159 159 159
Spacing : 160 160 160
Unit CellA = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.24 A , Y = 2.24 A , Z = 2.24 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.242.242.24
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-70-70-70
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.1051.8700.002
Annotation DetailsSurface rendered Rio2 depletion map
Supplement
Images
Images

1925.png
Sample
NameS. cerevisiae pre-40S ribosomal particle depleted for Rio2
Number of Components1
Theoretical Mass1.4 MDa
DetailsMonodisperse
Component #1: ribosome-eukaryote - pre-40S
Scientific namepre-40S
Theoretical Mass1.4 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesBaker's yeast
EukaryoteSSU 40S
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Conc1.5 mg/ml
Specimen Support Detailsquantifoil
Specimen Stateparticle
BufferDetails: 50mM Tris-Cl, 100mM NaCl, 10mM MgCl2, 0.075% NP40, 1mM imidazole, 2mM EGTA, 10 mM BME
pH: 7.5
Vitrification
MethodBlot for 2 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature85 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose16 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationCalibrated: 66964 X
AstigmatismObjective lens astigmatism was corrected at 135,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 4000 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder ( OTHER )
Temperature89 Kelvin ( 89 Kelvin - 89 Kelvin )
Camera
DetectorGatan US4000 CCD camera
Image Acquisition
Number of Digital Images240
Sampling Size2.24 microns
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
Euler Angles DetailsEMAN convention
SoftwareEMAN
CTF CorrectionEach micrograph
DetailsFinal map was filtered to 22A resolution
Resolution By Author22
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections7069
Detailsmanual particle selection
Download
Data from EMDB
Header (meta data in XML format)emd-1925.xml (7.3 KB)
Map dataemd_1925.map.gz (11.5 MB)
Images1925.png (77.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1925
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 27 KB