[English] 日本語
Yorodumi
- EMDB-1917: Intermediate binding positions of RRF and EF-G on the post-termin... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1917
TitleIntermediate binding positions of RRF and EF-G on the post-termination complex
KeywordsRibosome recycling factor / Elongation Factor G / T. thermophilus ribosome recycling factor / 70S / E. coli Post Termination Complex / cryo-EM
SampleT. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
Map dataE. coli 70S post-termination complex with bound Thermus thermophilus RRF and E. coli EF-G.
Methodsingle particle reconstruction, at 9.9 A resolution
AuthorsYokoyama T / Shaikh TR / Iwakura N / Kaji H / Kaji A / Agrawal RK
CitationEMBO J., 2012, 31, 1836-1846

EMBO J., 2012, 31, 1836-1846 StrPapers
Structural insights into initial and intermediate steps of the ribosome-recycling process.
Takeshi Yokoyama / Tanvir R Shaikh / Nobuhiro Iwakura / Hideko Kaji / Akira Kaji / Rajendra K Agrawal

DateDeposition: Jun 29, 2011 / Header (metadata) release: Jul 15, 2011 / Map release: Apr 27, 2012 / Last update: Jun 29, 2011

-
Structure visualization

Movie
  • Surface view with fitted model
  • Atomic models: : PDB-3j0e
  • Surface level: 272
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 272
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3j0e
  • Surface level: 272
  • 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_1917.map.gz (map file in CCP4 format, 8584 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.78 A/pix
= 361.4 A
130 pix
2.78 A/pix
= 361.4 A
130 pix
2.78 A/pix
= 361.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.78 A
Density
Contour Level:272 (by author), 272 (movie #1):
Minimum - Maximum-1350.87719727 - 3122.80712891
Average (Standard dev.)40.61297226 (297.30963135)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin000
Limit129129129
Spacing130130130
CellA=B=C: 361.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.782.782.78
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z361.400361.400361.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-1350.8773122.80740.613

-
Supplemental data

-
Sample components

-
Entire T. thermophilus Ribosome Recyling Factor and E. coli Elongation F...

EntireName: T. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
Number of components: 3 / Oligomeric State: Trimer
MassTheoretical: 2.5 MDa

-
Component #1: ribosome-prokaryote, 70S E. coli Post-Termination Complex

Ribosome-prokaryoteName: 70S E. coli Post-Termination Complex / a.k.a: 70S PoTC / Prokaryote: LSU 50S, SSU 30S / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #2: protein, Ribosome Recyling Factor

ProteinName: Ribosome Recyling Factor / a.k.a: RRF / Recombinant expression: Yes
SourceSpecies: Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス

-
Component #3: protein, Elongation Factor G

ProteinName: Elongation Factor G / a.k.a: EF-G / Recombinant expression: Yes
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.08 mg/ml
Buffer solution: 50mM Tris-HCl (pH 7.5), 10mM Mg(OAc)2, 25mM KCl
pH: 7.5
Support film300 mesh copper grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Details: Vitrification instrument: Vitrobot

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50310 X (calibrated) / Astigmatism: Objective correct at 200kX mag / Imaging mode: BRIGHT FIELD / Defocus: 400 - 4000 nm
Specimen HolderHolder: Side entry liquid nitrogen cooled cryo holder / Model: OTHER / Temperature: 80 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 383 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 338823 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: SPIDER / CTF correction: each micrograph / Resolution: 9.9 A / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Software: MDFF / Refinement protocol: flexible / Refinement space: REAL / Details: Protocol: Flexible Fitting
Input PDB model: 2AVY
Modeling #2Software: MDFF / Refinement protocol: flexible / Refinement space: REAL / Details: Protocol: Flexible Fitting
Input PDB model: 2AW4
Modeling #3Software: MDFF / Refinement protocol: flexible / Refinement space: REAL / Details: Protocol: Flexible Fitting
Input PDB model: 1EH1
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