3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1895

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, Image by UCSF CHIMERA

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

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1895
TitleCryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor
MapYjeQ in complex with the 30S ribosomal subunit
SampleEscherichia coli 30S ribosomal subunit in complex with the YjeQ protein
KeywordsRibosome assembly, 30S subunit, YjeQ protein, RsgA protein, GTPase
AuthorsJomaa A, Stewart G, Mears JA, Kireeva I, Brown ED, Ortega J
DateDeposition: 2011-04-18, Header release: 2011-05-27, Map release: 2011-10-28, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

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

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

Supplemental images
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
List of similar structure data Omokage searchabout 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.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.54 A/pix
= 325.12 A
128 pix
2.54 A/pix
= 325.12 A
128 pix
2.54 A/pix
= 325.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
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 orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 325.12 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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-160-160-159
NX/NY/NZ320320320
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
Sample
NameEscherichia coli 30S ribosomal subunit in complex with the YjeQ protein
Number of Components2
Theoretical Mass0.9MDa
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
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteSSU 30S
Recombinant expressionNo
Component #2: protein - Assembly factor
Scientific nameRsgA, YjeQ
Common NameAssembly factor
Experimental Mass0.039 MDa
Oligomeric DetailsMonomer
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainBW25113
Recombinant expressionYes
Natural SourceCell: Cytoplasm
Engineered SourceVector: pDEST17-YjeQ
NCBI taxonomy: 562
Expression system: Escherichia coli
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, Calibrated: 50000
AstigmatismCorrected at 200000 times magnification
Nominal Cs1 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
ModelGATAN LIQUID NITROGEN
Temperature100 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images150
Sampling Size2.54
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareXmipp
CTF CorrectionEach micrograph
Resolution By Author16.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections16228
DetailsParticles were picked with Boxer.
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body. Each domain of YjeQ was fitted separately
Refinement Protocolrigid body
Refinement SpaceREAL
Target CriteriaR-factor
SoftwareChimera
PDB Entry ID2AVY
Model #1
Refinement SpaceREAL
Target CriteriaR-factor
Refinement Protocolrigid body
DetailsProtocol: Rigid Body. Each domain of YjeQ was fitted separately
SoftwareChimera
PDB Entry ID2RCN
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1895.xml (9.2 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