[English] 日本語
Yorodumi
- PDB-3eq3: Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3eq3
TitleModel of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM
DescriptorElongation factor Tu
30S ribosomal protein S12
50S ribosomal protein L11/RNA complex
KeywordsRIBOSOMAL PROTEIN/RNA / protein translation / ternary complex / A/T-tRNA / automated data collection / Antibiotic resistance / Elongation factor / GTP-binding / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / RIBOSOMAL PROTEIN-RNA COMPLEX
Specimen sourceEscherichia coli k12 / bacteria / image: Escherichia coli
MethodElectron microscopy (9 Å resolution / Particle / Single particle)
AuthorsFrank, J. / Li, W. / Agirrezabala, X.
CitationEMBO J., 2008, 27, 3322-3331

EMBO J., 2008, 27, 3322-3331 StrPapers
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
Wen Li / Xabier Agirrezabala / Jianlin Lei / Lamine Bouakaz / Julie L Brunelle / Rodrigo F Ortiz-Meoz / Rachel Green / Suparna Sanyal / Måns Ehrenberg / Joachim Frank

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 30, 2008 / Release: Dec 16, 2008
RevisionDateData content typeGroupProviderType
1.0Dec 16, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2May 30, 2012Structure modelRefinement description

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1565
  • 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: Elongation factor Tu
L: 30S ribosomal protein S12
I: 50S ribosomal protein L11
Y: tRNA
A: Fragment h18 of the 16S rRNA
C: Fragment h44 of the 16S rRNA
B: Fragment H43-44 of the 23S rRNA
D: Fragment H95 of the 23S rRNA
E: Fragment H69 of the 23S rRNA


Theoretical massNumber of molelcules
Total (without water)131,9789
Polyers131,9789
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Polypeptide(L) , 3 types, 3 molecules XLI

#1: Polypeptide(L)Elongation factor Tu / EF-Tu / P-43 / Coordinate model: Cα atoms only


Mass: 43239.297 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12 / References: UniProt: P0A6N1

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)30S ribosomal protein S12 / Coordinate model: Cα atoms only


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12 / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S ribosomal protein L11 / Coordinate model: Cα atoms only


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12 / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

-
RNA chain , 6 types, 6 molecules YACBDE

#4: RNA chaintRNA / Coordinate model: P atoms only


Mass: 23844.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#5: RNA chainFragment h18 of the 16S rRNA / Coordinate model: P atoms only


Mass: 2871.766 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#6: RNA chainFragment h44 of the 16S rRNA / Coordinate model: P atoms only


Mass: 3601.218 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#7: RNA chainFragment H43-44 of the 23S rRNA / Coordinate model: P atoms only


Mass: 15504.268 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#8: RNA chainFragment H95 of the 23S rRNA / Coordinate model: P atoms only


Mass: 9089.461 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#9: RNA chainFragment H69 of the 23S rRNA / Coordinate model: P atoms only


Mass: 5427.285 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: ribosome in pre-accommodated state / Type: RIBOSOME
Details: A/T-tRNA(Trp), EF-Tu, L11, S12, fragments h44 and h18 from the 16S rRNA, fragments H43-H44, H69, and H95 from the 23S rRNA
Buffer solutionDetails: HiFi buffer (50 mM Tris-HCl pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: NITROGEN

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Jan 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GENERIC CCD

-
Processing

EM software
IDNameCategoryDetails
1RSRefMODEL FITTINGTNT
2SPIDERRECONSTRUCTION
SymmetryPoint symmetry: C1
3D reconstructionMethod: SINGLE PARTICLE / Resolution: 9 Å / Number of particles: 290000 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--See Method in the citation REFINEMENT PROTOCOL--auto
Ref protocol: OTHER / Ref space: REAL / Target criteria: cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting ID
12AVY1
22AW41
31QZA1
41OB21
Number of atoms included #LASTProtein: 657 / Nucleic acid: 187 / Ligand: 0 / Solvent: 0 / Total: 844

+
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