[English] 日本語
Yorodumi
- EMDB-1858: Structure of the ribosome-SecYE complex in the membrane environment -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1858
TitleStructure of the ribosome-SecYE complex in the membrane environment
SampleAn active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataThis map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc).
Methodsingle particle reconstruction, at 7.1 A resolution
AuthorsFrauenfeld J / Gumbart J / Sluis EO / Funes S / Gartmann M / Beatrix B / Mielke T / Berninghausen O / Becker T / Schulten K / Beckmann R
CitationNat. Struct. Mol. Biol., 2011, 18, 614-621

Nat. Struct. Mol. Biol., 2011, 18, 614-621 StrPapers
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
Jens Frauenfeld / James Gumbart / Eli O van der Sluis / Soledad Funes / Marco Gartmann / Birgitta Beatrix / Thorsten Mielke / Otto Berninghausen / Thomas Becker / Klaus Schulten / Roland Beckmann

DateDeposition: Jan 17, 2011 / Header (metadata) release: Apr 21, 2011 / Map release: Apr 21, 2011 / Last update: Jan 17, 2011

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4v6m
  • Surface level: 0.8
  • 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_1858.map.gz (map file in CCP4 format, 128001 KB)
Projections & slicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
320 pix
1.24 A/pix
= 396. A
320 pix
1.24 A/pix
= 396. A
320 pix
1.24 A/pix
= 396. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.2375 A
Density
Contour Level:0.5 (by author), 0.7 (movie #1):
Minimum - Maximum-3.53351 - 6.82334
Average (Standard dev.)0.0507365 (0.456442)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions320320320
Origin-160-160-159
Limit159159160
Spacing320320320
CellA=B=C: 396 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.23751.23751.2375
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S213
start NC/NR/NS-160-160-159
NC/NR/NS320320320
D min/max/mean-3.5346.8230.051

-
Supplemental data

-
Sample components

-
Entire An active E.coli SecYEG complex embedded in a lipid bilayer (Nano...

EntireName: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
Details: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc)
Number of components: 2
Oligomeric State: 70S ribosome bound to one copy of the E.coli SecYEG complex in a lipid bilayer
MassTheoretical: 2.7 MDa

-
Component #1: ribosome-prokaryote, 70S ribosome nascent chain complex

Ribosome-prokaryoteName: 70S ribosome nascent chain complex / a.k.a: 70S RNC / Prokaryote: ALL / Recombinant expression: No
MassTheoretical: 2.7 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #2: ligand, Nd-SecYEG

LigandName: Nd-SecYEG / a.k.a: SecYEG embedded in a Nanodisc / Oligomeric Details: Heterotrimeric / Recombinant expression: Yes / Number of Copies: 1
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Plasma membrane

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
pH: 7.2
VitrificationInstrument: NONE / Cryogen name: ETHANE

-
Electron microscopy imaging

ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal), 38000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4500 nm
Specimen HolderHolder: FEI Polara cartridge system / Model: OTHER
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionScanner: PRIMESCAN / Sampling size: 4.76 microns / Details: Scanned at 5334 dpi

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 85664 / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: SPIDER / CTF correction: Defocus group volumes / Resolution: 7.1 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