[English] 日本語
Yorodumi
- PDB-2akh: Normal mode-based flexible fitted coordinates of a non-translocat... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2akh
TitleNormal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli
DescriptorProtein-export membrane protein secG
Preprotein translocase secY subunit
Preprotein translocase secE subunit
KeywordsPROTEIN TRANSPORT / Protein transport / Translocation / Transmembrane / Transport
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (14.9 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsMitra, K.M. / Schaffitzel, C. / Shaikh, T. / Tama, F. / Jenni, S. / Brooks III, C.L. / Ban, N. / Frank, J.
CitationNature, 2005, 438, 318-324

Nature, 2005, 438, 318-324 StrPapers
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Kakoli Mitra / Christiane Schaffitzel / Tanvir Shaikh / Florence Tama / Simon Jenni / Charles L Brooks / Nenad Ban / Joachim Frank

DateDeposition: Aug 3, 2005 / Release: Nov 15, 2005 / Last modification: Feb 24, 2009

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1143
  • Imaged by Jmol
  • Download
3D viewer


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

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

Downloads & links

-
Assembly

Deposited unit
X: Protein-export membrane protein secG
Y: Preprotein translocase secY subunit
Z: Preprotein translocase secE subunit
A: Protein-export membrane protein secG
B: Preprotein translocase secY subunit
C: Preprotein translocase secE subunit


Theoretical massNumber of molelcules
Total (without water)127,9276
Polyers127,9276
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Polypeptide(L)Protein-export membrane protein secG / Preprotein translocase band 1 subunit / P12


Mass: 7906.411 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P33582

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)

Biological process

#2: Polypeptide(L)Preprotein translocase secY subunit


Mass: 43961.500 Da / Num. of mol.: 2 / Fragment: plug TMH 2a deleted / Mutation: DEL(40-75)
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P03844

Cellular component

Biological process

#3: Polypeptide(L)Preprotein translocase secE subunit


Mass: 12095.814 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P16920

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)

Biological process

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenName: protein-conducting channel / Aggregation state: PARTICLE
Component

Assembly id: 1 / Details: dimer of SecYEG heterotrimer / Go id: 0015450 / Name: protein translocase activity

IDIpr id
1IPR004692
2IPR002208
3IPR005807
VitrificationInstrument: two sided blotting plunger / Cryogen name: ETHANE / Temp: 93 K / Humidity: 90 / Method: Blot for 2 seconds before plunging

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F30 / Date: Mar 9, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 11 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 39000 X / Nominal defocus max: 4300 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Cryo Stage / Temperature: 93 K
CameraType: Kodak SO163 film
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: RSR2000
EM single particle entitySymmetry type: ASYMMETRIC
3D reconstructionResolution: 14.9 A / CTF correction method: defocus groups / Details: The resolution is based on FSC at 0.5 cut-off
Atomic model buildingMethod: normal mode-based flexible fitting / Software name: RSR2000
Ref protocol: normal mode-based flexible fitting, real space refinement
Ref space: REAL / Target criteria: correlation coefficient, R-factor
Number of atoms included #LASTProtein: 1176 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1176

+
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