PDB-1c2x: 5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1c2x
Title	5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION
Descriptor	5S RIBOSOMAL RNA
Keywords	RIBOSOME, 5S RRNA, 23S RRNA, LARGE RIBOSOMAL SUBUNIT, PROTEIN BIOSYNTHESIS, RIBONUCLEIC ACID, EM-RECONSTRUCTION, ATOMIC STRUCTURE, 3D ARRANGEMENT, FITTING
Authors	Brimacombe, R., Mueller, F.
Date	Deposition: 1999-07-28, Release: 2000-04-10
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	PDB-1c2w Cite PDB-487d Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-5242 PDB-1kvp PDB-3ixz PDB-1pn6 List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Mol. Biol., Vol. 298, Issue 1, Page 35-59, Year 2000
Title	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.
Authors	F 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.
Keywords	Base 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
Links	PubMed: 10756104, DOI: 10.1006/jmbi.2000.3635, PII: S0022-2836(00)93635-0
Citation - 1
Article	J.Mol.Biol., Vol. 271, Page: 524 - , Year: 1997,
Title	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
Authors	Mueller, F., Brimacombe, R.
Links	DOI: 10.1006/jmbi.1997.1210
Citation - 2
Article	J.Mol.Biol., Vol. 271, Page: 545 - , Year: 1997,
Title	A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. II. The RNA-Protein Interaction Data
Authors	Mueller, F., Brimacombe, R.
Links	DOI: 10.1006/jmbi.1997.1211
Citation - 3
Article	J.Mol.Biol., Vol. 271, Page: 566 - , Year: 1997,
Title	A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. III. The Topography of the Functional Centre
Authors	Mueller, F., Stark, H., Van Heel, M., Rinke-Appel, J., Brimacombe, R.
Links	DOI: 10.1006/jmbi.1997.1212

Components
ID 1 : 5S RRNA
Image
Description	5S RIBOSOMAL RNA
Type	polymer
Formula weight	38790.309 Da
Number of molecules	1
Details	THIRD OF THE 3 RRNA CHAINS OF THE RIBOSOME
Source	Method: Isolated from a natural source Genus: Escherichia Cellular location: CYTOPLASM NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Crystal
Description	THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

Electron Microscopy

Processing
Single particle entity
Symmetry type	ASYMMETRIC
3D fitting
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.
Refinement Space	REAL
Computing
Structure refinement	ERNA-3D
Refine
Ls d res high	7.50 A
ID	1
Refine hist
D res high	7.50
Total atoms	2570
Nucleic acid atoms	2570
Software
Classification	refinement
Name	ERNA-3D