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5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION

by single particle reconstruction, at 7.5 A resolution

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#1: Depositted structure unit, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsBrimacombe, R., Mueller, F.
DateDeposition: 1999-07-28, Release: 2000-04-10
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleJ. Mol. Biol., Vol. 298, Issue 1, Page 35-59, Year 2000
TitleThe 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.
AuthorsF Mueller, I Sommer, P Baranov, R Matadeen, M Stoldt, J Wöhnert, M Görlach, M van Heel, R Brimacombe
Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany.
KeywordsBase Sequence, Binding Sites, C-SAR protein, Aspergillus clavatus, Computer Simulation, Conserved Sequence (genetics), Cross-Linking Reagents, Cryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (chemistry), Fungal Proteins (metabolism), Microscopy, Immunoelectron, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, Peptide Elongation Factor Tu (metabolism, 3.6.1.-), RNA, Bacterial (chemistry), RNA, Ribosomal, 23S (chemistry), RNA, Ribosomal, 5S (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribonucleases (metabolism, 3.1.-), Ribosomal Proteins (metabolism), Ribosomes (chemistry), Ricin (metabolism, 9009-86-3), Thermodynamics, ribosomal protein L11
LinksPubMed: 10756104, DOI: 10.1006/jmbi.2000.3635, PII: S0022-2836(00)93635-0
Citation - 1
ArticleJ.Mol.Biol., Vol. 271, Page: 524 - , Year: 1997,
TitleA 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
AuthorsMueller, F., Brimacombe, R.
LinksDOI: 10.1006/jmbi.1997.1210
Citation - 2
ArticleJ.Mol.Biol., Vol. 271, Page: 545 - , Year: 1997,
TitleA New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. II. The RNA-Protein Interaction Data
AuthorsMueller, F., Brimacombe, R.
LinksDOI: 10.1006/jmbi.1997.1211
Citation - 3
ArticleJ.Mol.Biol., Vol. 271, Page: 566 - , Year: 1997,
TitleA New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. III. The Topography of the Functional Centre
AuthorsMueller, F., Stark, H., Van Heel, M., Rinke-Appel, J., Brimacombe, R.
LinksDOI: 10.1006/jmbi.1997.1212
Components
ID 1 : 5S RRNA
Image
Description5S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight38790.309 Da
Number of molecules1
ID1
DetailsTHIRD OF THE 3 RRNA CHAINS OF THE RIBOSOME
SourceMethod: Isolated from a natural source
Genus: Escherichia
Cellular location: CYTOPLASM
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Experiment
MethodELECTRON MICROSCOPY
Crystal
DescriptionTHE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.
Electron Microscopy
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D fitting
DetailsTHIS 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.
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
3D fitting list
3D Fitting ID1
Computing
Structure refinementERNA-3D
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.50 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.50
Total atoms2570
Nucleic acid atoms2570
Software
Ordinal1
Classificationrefinement
NameERNA-3D
Download
PDB format
Allpdb1c2x.ent.gz
pdb1c2x.ent (uncompressed file)
Header onlypdb1c2x.ent.gz
mmCIF format
mmCIF1c2x.cif.gz
XML format
All1c2x.xml.gz
No-atom1c2x-noatom.xml.gz
Ext-atom1c2x-extatom.xml.gz
Movie files
movie #1
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