Biological Assembly 1  

 3D View: Structure

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 941718.50 
• Atom Count: 62348 
• Residue Count: 2904 
• Unique nucleic acid chains: 1

1C2W

23S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION

• DOI: 10.2210/pdb1C2W/pdb

• Classification: RIBOSOME
• Organism(s): Escherichia coli


• Deposited: 1999-07-28 Released: 2000-04-10 
• Deposition Author(s): Brimacombe, R., Mueller, F.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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.

Mueller, F., Sommer, I., Baranov, P., Matadeen, R., Stoldt, M., Wohnert, J., Gorlach, M., van Heel, M., Brimacombe, R.

(2000) J.Mol.Biol. 298: 35-59

• PubMed: 10756104 
• DOI: 10.1006/jmbi.2000.3635
• Primary Citation of Related Structures:  
  487D, 1C2X


• PubMed Abstract: 
  

The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross-linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure.

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Related Citations: 

• A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. II. The RNA-Protein Interaction Data
  Mueller, F.,Brimacombe, R.
  (1997) J.Mol.Biol. 271: 545
• 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.
  (1999) Structure 7: 1575
• 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.
  (1997) J.Mol.Biol. 271: 524
• 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.
  (1997) J.Mol.Biol. 271: 566




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Organizational Affiliation: 

Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
23S RIBOSOMAL RNA	B	2904	Escherichia coli

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	B	RNA LINKING	C9 H13 N2 O9 P		U
5MC	B	RNA LINKING	C10 H16 N3 O8 P		C
1MA	B	RNA LINKING	C11 H16 N5 O7 P		A
7MG	B	RNA LINKING	C11 H18 N5 O8 P		G
5MU	B	RNA LINKING	C10 H15 N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
ERNA-3D	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-28 
• Released Date: 2000-04-10 
• Deposition Author(s): Brimacombe, R., Mueller, F.

Revision History 

• Version 1.0: 2000-04-10
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance