[English] 日本語
Yorodumi
- PDB-3izq: Structure of the Dom34-Hbs1-GDPNP complex bound to a translating ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3izq
TitleStructure of the Dom34-Hbs1-GDPNP complex bound to a translating ribosome
DescriptorProtein DOM34
Elongation factor 1 alpha-like protein
KeywordsRIBOSOMAL PROTEIN / HYDROLASE / No-Go mRNA decay
Specimen sourceSaccharomyces cerevisiae / yeast / brewer's yeast / yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (9.5 Å resolution / Particle / Single particle)
AuthorsBecker, T. / Armache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Sieber, H. / Abdel Motaal, B. / Mielke, T. / Berninghausen, O. / Beckmann, R.
CitationNat. Struct. Mol. Biol., 2011, 18, 715-720

Nat. Struct. Mol. Biol., 2011, 18, 715-720 StrPapers
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
Thomas Becker / Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Heidemarie Sieber / Basma Abdel Motaal / Thorsten Mielke / Otto Berninghausen / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 30, 2010 / Release: Jun 1, 2011
RevisionDateData content typeGroupProviderType
1.0Jun 1, 2011Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1811
  • 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
0: Protein DOM34
1: Elongation factor 1 alpha-like protein


Theoretical massNumber of molelcules
Total (without water)112,9462
Polyers112,9462
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Polypeptide(L)Protein DOM34 / Dom34p


Mass: 44119.797 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P33309, EC: 3.1.-.-

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Elongation factor 1 alpha-like protein / Hbs1p


Mass: 68826.406 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P32769

Cellular component

Molecular function

Biological process

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent ID
1Ribosome-bound Dom34-Hbs1-GDPNP complexRIBOSOME0
2No-Go mRNA decay factor1
Buffer solutionpH: 7
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Carbon-coated Quantifoil with 2 nm carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Details: Blotted for 10 seconds before plunging, used 2 layer of filter paper

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 / Calibrated magnification: 39000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1300 nm / Cs: 2.26 mm
Specimen holderTemperature: 84 kelvins
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 41
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1MDFFMODEL FITTING
2SPIDERRECONSTRUCTION
SymmetryPoint symmetry: C1
3D reconstructionMethod: Single particle projection-matching / Resolution: 9.5 Å / Number of particles: 38400 / Nominal pixel size: 1.2375 / Actual pixel size: 1.2375 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Number of atoms included #LASTProtein: 7183 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7183

+
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