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

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.5, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1924
TitleRibosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates
MapSurface rendered Ltv1 deletion map
SampleS. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
Keywordspre-40S, 40S intermediate, Ltv1 deletion
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: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.5, Made by UCSF CHIMERA

Supplemental images
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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_1924.map.gz ( map file in CCP4 format, 16001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.24 A/pix
= 358.4 A
160 pix
2.24 A/pix
= 358.4 A
160 pix
2.24 A/pix
= 358.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.3 (by author), 0.5 (movie #1):
Minimum - Maximum: -2.1019 - 3.94117
Average (Standard dev.): 0.0028384 (0.359594)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
Unit CellA= B= C: 358.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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-56-56-55
NX/NY/NZ112112112
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-2.1023.9410.003
Annotation DetailsSurface rendered Ltv1 deletion map
Supplement
Images
Images
Sample
NameS. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
Number of Components1
Theoretical Mass1.4MDa
DetailsMonodisperse
Component #1: ribosome-eukaryote - pre-40S
Scientific namepre-40S
Theoretical Mass1.4 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBakers' yeast
NCBI taxonomy4932
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
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
ModelOTHER
Temperature89 K ( 89 - 89 K)
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Image Acquisition
Number of Digital Images350
Sampling Size2.24
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
Euler Angles DetailsEMAN convention
SoftwareEMAN
CTF CorrectionEach micrograph
DetailsFinal map was filtered to 20A resolution
Resolution By Author20 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections10235
DetailsManual particle selection
Atomic Model Fitting
Model #0
Target CriteriaCC
DetailsProtocol: MDFF
SoftwareNAMD
Refinement Protocolflexible
Refinement SpaceREAL
PDB Entry ID3O2Z
Download
Data from EMDB
Header (meta data in XML format)emd-1924.xml (7.6 KB)
Map dataemd_1924.map.gz (11.4 MB)
Images1924.png (91.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1924
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.5 KB