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-1615

Three-dimensional structure of YidC bound to the translating ribosome

by single particle reconstruction, at 14.4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 40, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 40, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1615
TitleThree-dimensional structure of YidC bound to the translating ribosome
MapThis map shows YidC bound to the tunnel exit region of an ribosome nascent chain complex
SampleYidC bound to a translating ribosome
Keywordsmembrane protein insertion, ribosome, translation
AuthorsKohler R, Boehringer D, Greber B, Bingel-Erlenmeyer R, Collinson I, Schaffitzel C, Ban N
DateDeposition: 2009-04-23, Header release: 2009-04-28, Map release: 2010-09-10, Last update: 2010-09-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 40, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 40, Made by UCSF CHIMERA

Supplemental images

1615_1615.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1616
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1541

EMDB-1055

EMDB-1261

EMDB-1056

EMDB-1248

EMDB-5234
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleMol. Cell, Vol. 34, Issue 3, Page 344-53, Year 2009
TitleYidC and Oxa1 form dimeric insertion pores on the translating ribosome.
AuthorsRebecca Kohler, Daniel Boehringer, Basil Greber, Rouven Bingel-Erlenmeyer, Ian Collinson, Christiane Schaffitzel, Nenad Ban
Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
KeywordsBacterial Proteins (chemistry), Cysteine (chemistry, 52-90-4), Dimerization, Electron Transport Complex IV (chemistry, 1.9.3.1), Escherichia coli Proteins (chemistry), Membrane Transport Proteins (chemistry), Mitochondrial Proteins (chemistry), Models, Molecular, Multiprotein Complexes (metabolism), Nuclear Proteins (chemistry), OXA1 protein, Oxidation-Reduction, Protein Binding, Protein Biosynthesis, Protein Structure, Quaternary, Ribosomes (genetics), SecY protein, E coli, YIDC protein, E coli
LinksPII: S1097-2765(09)00272-X, DOI: 10.1016/j.molcel.2009.04.019, PubMed: 19450532
Map
FileEMD-1615.map ( map file in CCP4 format, 5040 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:40 (by author), 40 (movie #1):
Minimum - Maximum: -191.38 - 342.407
Average (Standard dev.): 2.54968 (27.2976)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 108 108 108
Origin : 0 0 0
Limit : 107 107 107
Spacing : 108 108 108
Unit CellA = 406.08 A , B = 406.08 A , C = 406.08 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 3.76 A , Y = 3.76 A , Z = 3.76 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.763.763.76
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z406.080406.080406.080
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108108108
start NC,NX/NR,NY/NS,NZ000
NC,NX/NR,NY/NS,NZ108108108
D min/max/mean-191.380342.4072.550
Annotation DetailsThis map shows YidC bound to the tunnel exit region of an ribosome nascent chain complex
Supplement
Images
Images

1615_1615.png
Sample
NameYidC bound to a translating ribosome
Number of Components2
Theoretical Mass2.6 MDa
Experimental Mass2.6 MDa
Component #1: ribosome-prokaryote - Translating ribosome
Scientific nameRibosome nascent chain complex
Common NameTranslating ribosome
Theoretical Mass2.6 MDa
Experimental Mass2.6 MDa
ProkaryoteALL
Component #2: protein - Membrane protein insertase
Scientific nameYidC
Common NameMembrane protein insertase
Theoretical Mass62 MDa
Experimental Mass62 MDa
Oligomeric DetailsDimer
Number of Copies2
Scientific Name of SpeciesEscherichia coli (NCBI Taxonomy: 562)

StrainK-12
Recombinant expressionYes
Natural SourceCell Location: Membrane
Engineered SourceVector: peT24a
Exp System: Escherichia coli (NCBI Taxonomy: 562)
LinksInterPro: IPR:013308, Gene Ontology: GO:0051205
Experiment
Sample Preparation
Specimen Support Details200 mesh copper
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: Plunger
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI TECNAI 20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 4000 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Sampling Size12.7 microns
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmProjection matching
SoftwareImagic-5 Spider
CTF CorrectionEach image
Resolution By Author14.4
Resolution MethodFSC at 0.5 (extrapolated to full the full dataset)
Single Particle
Number of Projections24395
Download
Data from EMDB
Header (meta data in XML format)emd-1615.xml (7.7 KB)
Map dataemd_1615.map.gz (4.5 MB)
Images1615_1615.png (175.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1615
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, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.4 KB