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Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.

by single particle reconstruction, at 15.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 60, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 60, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1zn0, PDB-1zn1, Surface level: 60, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1zn0, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1zn1, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1127
TitleMechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
MapThis is a 50S.EF-G.GDPNP.RRF complex from E.coli
Sample50S.EF-G.GDPNP.RRF complex from E.coli
AuthorsGao N, Zavialov AV, Li W, Sengupta J, Valle M, Gursky RP, Ehrenberg M, Frank J
DateDeposition: 2005-05-11, Header release: 2005-05-11, Map release: 2006-05-11, Last update: 2012-10-31
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 60, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 60, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1zn0, PDB-1zn1, Surface level: 60, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1zn0, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1zn1, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-1zn0

CiteFit

PDB-1zn1

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
ArticleMol. Cell, Vol. 18, Issue 6, Page 663-74, Year 2005
TitleMechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
AuthorsNing Gao, Andrey V Zavialov, Wen Li, Jayati Sengupta, Mikel Valle, Richard P Gursky, Måns Ehrenberg, Joachim Frank
Wadsworth Center, State University of New York at Albany, Empire State Plaza, Albany, New York 12201, USA.
KeywordsCryoelectron Microscopy (methods), Image Processing, Computer-Assisted, Models, Molecular, Molecular Conformation, Peptide Chain Termination, Translational, Peptide Elongation Factor G (metabolism), Protein Conformation, Protein Structure, Secondary, RNA, Messenger (chemistry), Ribosomal Proteins (metabolism), ribosome releasing factor
LinksPII: S1097-2765(05)01311-0, DOI: 10.1016/j.molcel.2005.05.005, PubMed: 15949441
Map
Fileemd_1127.map.gz ( map file in CCP4 format, 8584 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:55.3, 60 (movie #1):
Minimum - Maximum: -123.87 - 336.361
Average (Standard dev.): 3.60572 (29.4095)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin-65-65-65
Limit646464
Spacing130130130
Unit CellA= B= C: 366.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.82 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-123.870336.3613.606
Annotation DetailsThis is a 50S.EF-G.GDPNP.RRF complex from E.coli
Supplement
Images
Images
Sample
Name50S.EF-G.GDPNP.RRF complex from E.coli
Number of Components3
Component #1: ribosome-prokaryote - 50S subunit
Scientific name50S subunit
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteLSU 50S
Recombinant expressionNo
Component #2: protein - RRF
Scientific nameRRF
Number of Copies1
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Recombinant expressionNo
Component #3: protein - EF-G
Scientific nameEF-G
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Recombinant expressionNo
Experiment
Sample Preparation
StainingCryo-EM
Specimen Support DetailsQuantifoil holley carbon film grids
Specimen Stateparticle
BufferDetails: polymix buffer
pH: 7.5
Vitrification
Cryogen NameETHANE
Humidity90
Temperature93 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 2 seconds before plunging
DetailsVitrification instrument: two-sided blotting plunger
Imaging
MicroscopeFEI TECNAI F20
Date2003-02-01
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 49700
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 4800 nm
Specimen Holder
HolderCryo transfer
ModelGATAN LIQUID NITROGEN
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Sampling Size14
Od Range1.2
Quant Bit Number12
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmreference projection
SoftwareSPIDER
CTF Correctiondefocus groups
Resolution By Author15.5 A
Resolution MethodFSC 0.5
DetailsAmplitude correction was applied using low-angle x-ray scattering data.
Single Particle
Number of Projections32171
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1127.xml (7.9 KB)
Map dataemd_1127.map.gz (7.9 MB)
Images1127.gif (30.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1127
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, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 268.4 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.9 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.2 MB