[English] 日本語
Yorodumi
- PDB-2ix8: MODEL FOR EEF3 BOUND TO AN 80S RIBOSOME -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2ix8
TitleMODEL FOR EEF3 BOUND TO AN 80S RIBOSOME
DescriptorELONGATION FACTOR 3A
KeywordsNUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / PHOSPHORYLATION / ELONGATION FACTOR / RNA-BINDING / ATP-BINDING / RRNA-BINDING
Specimen sourceSaccharomyces cerevisiae / yeast / BAKER'S YEAST / サッカロミセス・セレビシエ /
MethodElectron microscopy (9.9 Å resolution / Particle / Single particle)
AuthorsAndersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. / Kinzy, T.G. / Andersen, G.R. / Beckmann, R.
CitationNature, 2006, 443, 663-668

Nature, 2006, 443, 663-668 StrPapers
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss Kinzy / Gregers R Andersen / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 7, 2006 / Release: Jul 10, 2007
RevisionDateData content typeGroupProviderType
1.0Jul 10, 2007Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1233
  • 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
A: ELONGATION FACTOR 3A


Theoretical massNumber of molelcules
Total (without water)109,4421
Polyers109,4421
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

-
Components

#1: Polypeptide(L)ELONGATION FACTOR 3A / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION FACTOR 3 / EEF3 / YEAST ELONGATION FACTOR 3


Mass: 109441.547 Da / Num. of mol.: 1
Details: TRANSLATION ELONGATION IN FUNGI ABC-TYPE ATPASE TRNA RELEASE
Fragment: RESIDUES 1-976
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P16521

Cellular component

Molecular function

Biological process

Sequence detailsPDB LACKS THE C-TERMINAL PART OF EEF3 (RESIDUES 977-1044)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: 80S-RNC-EEF3-AMP-PNP COMPLEX / Type: RIBOSOME
Buffer solutionName: 20MM HEPES,PH 7.5,10MM MG(OAC)2,150MM KOAC 1MM DTT,0.05% NIKKOL, 125MM SUCROSE,0.01MG -ML-1 CYCLOHEXIMIDE,0.5MM AMP-PNP,0.1MM NEOMYCIN, 0.3% DESOXYBIGCHAPS
Details: 20MM HEPES,PH 7.5,10MM MG(OAC)2,150MM KOAC 1MM DTT,0.05% NIKKOL, 125MM SUCROSE,0.01MG -ML-1 CYCLOHEXIMIDE,0.5MM AMP-PNP,0.1MM NEOMYCIN, 0.3% DESOXYBIGCHAPS
pH: 7.5
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Feb 11, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 / Calibrated magnification: 38900 / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 95 kelvins / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 141
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1OMODEL FITTING
2SitusMODEL FITTING
3SPIDERRECONSTRUCTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 37700 / Symmetry type: POINT
Least-squares processHighest resolution: 6 Å
Refine hist #LASTHighest resolution: 6 Å
Number of atoms included #LASTProtein: 7599 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7599

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
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

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