[English] 日本語
Yorodumi
- PDB-1c2x: 5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1c2x
Title5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION
Descriptor5S RIBOSOMAL RNA
KeywordsRIBOSOME / 5S RRNA / 23S RRNA / LARGE RIBOSOMAL SUBUNIT / PROTEIN BIOSYNTHESIS / RIBONUCLEIC ACID / EM-RECONSTRUCTION / ATOMIC STRUCTURE / 3D ARRANGEMENT / FITTING
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.5 Å resolution / Particle / Single particle)
AuthorsBrimacombe, R. / Mueller, F.
CitationJ. Mol. Biol., 2000, 298, 35-59

primary. J. Mol. Biol., 2000, 298, 35-59 Yorodumi Papers
The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.
F Mueller / I Sommer / P Baranov / R Matadeen / M Stoldt / J Wöhnert / M Görlach / M van Heel / R Brimacombe

#1. J.Mol.Biol., 1997, 271, 524-
A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. I. Fitting the RNA to a 3D Electron Microscopic Map at 20 Angstroms
Mueller, F. / Brimacombe, R.

#2. J.Mol.Biol., 1997, 271, 545-
A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. II. The RNA-Protein Interaction Data
Mueller, F. / Brimacombe, R.

#3. J.Mol.Biol., 1997, 271, 566-
A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. III. The Topography of the Functional Centre
Mueller, F. / Stark, H. / Van Heel, M. / Rinke-Appel, J. / Brimacombe, R.

#4. Structure, 1999, 7, 1575-
The Escherichia coli large ribosomal subunit at 7.5 A resolution
Matadeen, R. / Patwardhan, A. / Gowen, B. / Orlova, E.V. / Pape, T. / Cuff, M. / Mueller, F. / Brimacombe, R. / van Heel, M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 28, 1999 / Release: Apr 10, 2000
RevisionDateData content typeGroupProviderType
1.0Apr 10, 2000Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Movie
  • Deposited structure unit
  • 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
C: 5S RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)38,7901
Polyers38,7901
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: RNA chain5S RIBOSOMAL RNA / 5S RRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Details: THIRD OF THE 3 RRNA CHAINS OF THE RIBOSOME
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 50S Ribosomal Subunit / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
CrystalDescription: THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG / Details: from Structure 1999 citation
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingFilm or detector model: GENERIC FILM
Image scansScanner model: IMAGE SCIENCE PATCHWORK DENSITOMETER

-
Processing

SoftwareName: ERNA-3D / Classification: refinement
EM softwareName: IMAGIC / Version: 5 / Category: CTF CORRECTION
Particle selectionDetails: from seven micrographs / Number of particles selected: 16000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number of particles: 16000 / Symmetry type: POINT
Atomic model buildingDetails: DETAILS--THIS FILE HAS BEEN GENERATED BY THE USE OF ALL RELEVANT BIOCHEMICAL CONSTRAINTS AND THE CONSTRAINTS GIVEN BY THE ELECTRON DENSITY CONTOUR OF THE RIBOSOME, WHICH WAS DERIVED FROM THE CRYO-ELECTRON MICROSCOPIC RECONSTRUCTION. THIS FILE IS PART OF A SET OF ALL THREE RIBONUCLEIC ACID CHAINS OF THE RIBOSOME TOGETHER WITH A NUMBER OF RIBOSOMAL PROTEINS WHICH ARE ALSO DEPOSITED WITH THE PDB DATA BANK. THE ATOMIC COORDINATES OF ALL THESE RIBOSOMAL COMPONENTS REFLECT THEIR POSITIONS IN THE 70S RIBOSOME.
Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11CSV1
21CSW1
Least-squares processHighest resolution: 7.5 Å
Refine hist #LASTHighest resolution: 7.5 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 2576 / Ligand: 0 / Solvent: 0 / Total: 2576

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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)

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