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Cryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor

by single particle reconstruction, at 16.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0088, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.0088, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4a2i, Surface level: 0.0088, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1895
AuthorsJomaa A, Stewart G, Mears JA, Kireeva I, Brown ED, Ortega J
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0088, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.0088, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4a2i, Surface level: 0.0088, Made by UCSF CHIMERA

Supplemental images

YjeQ+30S.tif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-4a2i
CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)

Diagram

EMDB-1413

EMDB-1774

EMDB-2017

PDB-3j28

EMDB-2020

EMDB-1346
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleRNA, Vol. 17, Issue 11, Page 2026-38, Year 2011
TitleCryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor.
AuthorsAhmad Jomaa, Geordie Stewart, Jason A Mears, Inga Kireeva, Eric D Brown, Joaquin Ortega
Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada.
KeywordsCryoelectron Microscopy, Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), GTP Phosphohydrolases (chemistry, 3.6.1.-), Models, Molecular, Protein Binding, Protein Structure, Tertiary, Ribosome Subunits, Small, Bacterial (chemistry), YjeQ protein, E coli (3.6.1.-)
LinksDOI: 10.1261/rna.2922311, PubMed: 21960487, PMC: PMC3198595
Map
FileEMD-1895.map ( map file in CCP4 format, 8390 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:0.0088 (by author), 0.0088 (movie #1):
Minimum - Maximum: -0.0217409 - 0.0623605
Average (Standard dev.): 0.000295723 (0.00440148)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : 0 0 0
Limit : 127 127 127
Spacing : 128 128 128
Unit CellA = 325.12 A , B = 325.12 A , C = 325.12 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.54 A , Y = 2.54 A , Z = 2.54 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.542.542.54
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z325.120325.120325.120
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/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0220.0620.000
Annotation DetailsYjeQ in complex with the 30S ribosomal subunit
Supplement
Images
Images

YjeQ+30S.tif
Sample
NameEscherichia coli 30S ribosomal subunit in complex with the YjeQ protein
Number of Components2
Theoretical Mass0.9 MDa
Details30S was mixed with YjeQ in 1-to-5 molar ratio
Component #1: ribosome-prokaryote - 30S subunit
Scientific name30S ribosomal subunit
Common Name30S subunit
Theoretical Mass0.9 MDa
ProkaryoteSSU 30S
Component #2: protein - Assembly factor
Scientific nameRsgA, YjeQ
Common NameAssembly factor
Experimental Mass39 MDa
Oligomeric DetailsMonomer
Scientific Name of SpeciesEscherichia coli (NCBI Taxonomy: 562)

StrainBW25113
Recombinant expressionYes
Natural SourceCell: Cytoplasm
Engineered SourceVector: pDEST17-YjeQ
Exp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc0.9 mg/ml
Specimen Support Details200 mesh copper grid
Specimen Stateparticle
BufferDetails: 10 mM Tris-HCl pH 7.5, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol.
pH: 7.5
Vitrification
MethodBlot for 7 seconds
Cryogen NameETHANE
DetailsVitrification instrument: FEI Vitrobot III
Humidity100
InstrumentFEI VITROBOT MARK III
Temperature100 Kelvin
Imaging
MicroscopeJEOL 2010F
Date12-May-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
AstigmatismCorrected at 200000 times magnification
Nominal Cs1.0 mm
Imaging ModeBRIGHT FIELD
Defocus650 nm - 3900 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder.This holder operates in the temperature range from -175 C to ambient ( GATAN LIQUID NITROGEN )
Temperature100 Kelvin
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images150
Sampling Size2.54 microns
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmProjection matching
SoftwareXmipp
CTF CorrectionEach micrograph
Resolution By Author16.5
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections16228
DetailsParticles were picked with Boxer.
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body. Each domain of YjeQ was fitted separately
Refinement Protocolrigid body
Refinement SpaceREAL
Target CriteriaR-factor
SoftwareChimera
Model #1
Refinement SpaceREAL
Target CriteriaR-factor
Refinement Protocolrigid body
DetailsProtocol: Rigid Body. Each domain of YjeQ was fitted separately
SoftwareChimera
Fitted Coordinate
PDB entry ID

PDB-4a2i
Download
Data from EMDB
Header (meta data in XML format)emd-1895.xml (9 KB)
Map dataemd_1895.map.gz (7.4 MB)
ImagesYjeQ+30S.tif (136.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1895
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.6 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, 26.7 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 13.6 MB