[English] 日本語
Yorodumi
- EMDB-1724: Ribosome dynamics and tRNA movement as visualized by time-resolve... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1724
TitleRibosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy
KeywordsRibosome / translation / translocation / tRNA
SampleSubstate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Synthetic construct
Map dataSubstate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
Methodsingle particle reconstruction, at 9 A resolution
AuthorsFischer N / Konevega AL / Wintermeyer W / Rodnina MV / Stark H
CitationNature, 2010, 466, 329-333

Nature, 2010, 466, 329-333 StrPapers
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
Niels Fischer / Andrey L Konevega / Wolfgang Wintermeyer / Marina V Rodnina / Holger Stark

DateDeposition: Apr 30, 2010 / Header (metadata) release: May 13, 2010 / Map release: May 6, 2011 / Last update: Apr 30, 2010

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 40
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 40
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4v7a
  • Surface level: 40
  • 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_1724.map.gz (map file in CCP4 format, 27649 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.87 A/pix
= 359.04 A
192 pix
1.87 A/pix
= 359.04 A
192 pix
1.87 A/pix
= 359.04 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.87 A
Density
Contour Level:40 (by author), 40 (movie #1):
Minimum - Maximum-122.023 - 223.953
Average (Standard dev.)-0.755981 (22.4777)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 359.04 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.871.871.87
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z359.040359.040359.040
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-122.023223.953-0.756

-
Supplemental data

-
Sample components

-
Entire Substate of E. coli 70S-fMetVal-tRNAVal post-translocation comple...

EntireName: Substate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
Number of components: 3
MassTheoretical: 2.5 MDa

-
Component #1: ribosome-prokaryote, Ribosome

Ribosome-prokaryoteName: Ribosome / a.k.a: E. coli 70S / Prokaryote: ALL / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #2: nucleic-acid, fMetVal-tRNAVal

Nucleic-acidName: fMetVal-tRNAVal / a.k.a: peptidyl tRNA / Class: T-RNA / Structure: DOUBLE HELIX / Synthetic: No
MassTheoretical: 25 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #3: nucleic-acid, m022 mRNA

Nucleic-acidName: m022 mRNA / a.k.a: mRNA / Class: RNA / Details: Coding sequence AUGGUU / Structure: SINGLE STRANDED / Synthetic: Yes
SourceSpecies: Synthetic construct

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
pH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 75 % / Method: Manual blotting for about 2 seconds
Details: Vitrification instrument: Custom-built CEVS. Dew-point temperature (temperature on the grid) adjusted to 18 degrees C

-
Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
LensMagnification: 161000 X (nominal), 162740 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 2000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 77 K
CameraDetector: GENERIC TVIPS (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 26429 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: IMAGIC, custom, Spider / CTF correction: Local / Resolution: 9 A / Resolution method: FSC 0.5

-
Atomic model buiding

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