[English] 日本語
Yorodumi
- EMDB-5386: tmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5386
TitletmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex
Keywordstrans-translation / MLD-loading / translocation / tmRNA / EF-G / SmpB
SampleComplex of 70S-tmRNA-SmpB-EF-G
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataOverall view of the 70S-tmRNA-SmpB-EF-G complex
Methodsingle particle reconstruction, at 8.3 A resolution
AuthorsRamrath DJF / Yamamoto H / Rother K / Wittek D / Pech M / Mielke T / Loerke J / Scheerer P / Ivanov P / Teraoka Y / Shpanchenko O / Nierhaus KH / Spahn CMT
CitationNature, 2012, 485, 526-529

Nature, 2012, 485, 526-529 StrPapers
The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
David J F Ramrath / Hiroshi Yamamoto / Kristian Rother / Daniela Wittek / Markus Pech / Thorsten Mielke / Justus Loerke / Patrick Scheerer / Pavel Ivanov / Yoshika Teraoka / Olga Shpanchenko / Knud H Nierhaus / Christian M T Spahn

DateDeposition: Jan 20, 2012 / Header (metadata) release: Feb 21, 2012 / Map release: Apr 30, 2012 / Last update: Jan 20, 2012

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4v6t
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_5386.map.gz (map file in CCP4 format, 105470 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.26 A/pix
= 378. A
300 pix
1.26 A/pix
= 378. A
300 pix
1.26 A/pix
= 378. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.26 A
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-3.38914657 - 9.00063801
Average (Standard dev.)0.20524462 (0.75120121)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
CellA=B=C: 378 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.261.261.26
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-3.3899.0010.205

-
Supplemental data

-
Sample components

-
Entire Complex of 70S-tmRNA-SmpB-EF-G

EntireName: Complex of 70S-tmRNA-SmpB-EF-G / Details: the sample was flash frozen in liquid ethane / Number of components: 5 / Oligomeric State: Monomer
MassTheoretical: 3 MDa / Experimental: 3 MDa / Measured by: Sedimentation

-
Component #1: ribosome-prokaryote, Ribosome

Ribosome-prokaryoteName: Ribosome / a.k.a: 70S-tmRNA-EFG / Details: the complex was stalled with fusidic acid / Prokaryote: ALL / Recombinant expression: No
MassTheoretical: 3.05 MDa / Experimental: 3 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: CAN20

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.15 mg/ml
Buffer solution: 20 mM HEPES-KOH, pH 7.6, 4.5 mM Mg(Ac)2, 150 mM NH4Ac, 4 mM b-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine
pH: 7.6
Support filmQuantifoil R3-3 Cu 300 mesh with 2 nm carbon support film
Stainingflash frozen in liquid ethane
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 96.15 K / Humidity: 100 % / Method: blot for 10 seconds before plunging / Details: Vitrification instrument: FEI VITROBOT

-
Electron microscopy imaging

ImagingMicroscope: FEI POLARA 300 / Date: Dec 8, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
LensMagnification: 39000 X (nominal), 39000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
Specimen HolderHolder: Cartridge / Model: GATAN HELIUM / Temperature: 77.15 K ( 77.15 - 81.15 K)
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 302 / Scanner: PRIMESCAN / Sampling size: 4.7 microns / Bit depth: 16

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 68842 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: angular refinement / Software: Spider / CTF correction: Defocus groups / Resolution: 8.3 A / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: cross-correlation / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 3R8S
Output model

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more