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- PDB-1c2w: 23S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7... -

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Entry
Database: PDB / ID: 1c2w
Title23S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION
Components23S RIBOSOMAL RNA
KeywordsRIBOSOME / 23S RRNA / LARGE RIBOSOMAL SUBUNIT / ATOMIC PROTEIN BIOSYNTHESIS / RIBONUCLEIC ACID / EM-RECONSTRUCTION / 3D ARRANGEMENT / FITTING
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsBrimacombe, R. / Mueller, F.
Citation
Journal: J Mol Biol / 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 /
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 ...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.
#1: Journal: J.Mol.Biol. / 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.
#2: Journal: J.Mol.Biol. / 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.
#3: Journal: J.Mol.Biol. / 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.
#4: Journal: Structure / Year: 1999
Title: The Escherichia coli large ribosomal subunit at 7.5 A resolution
Authors: Matadeen, R. / Patwardhan, A. / Gowen, B. / Orlova, E.V. / Pape, T. / Cuff, M. / Mueller, F. / Brimacombe, R. / van Heel, M.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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Assembly

Deposited unit
B: 23S RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)941,7191
Polymers941,7191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain 23S RIBOSOMAL RNA / / 23S RRNA


Mass: 941718.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SECOND OF THE 3 RRNA CHAINS OF THE RIBOSOME / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

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

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Electron microscopy imaging

MicroscopyModel: 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 FIELDBright-field microscopy / Nominal magnification: 38000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingFilm or detector model: GENERIC FILM / Num. of real images: 7
Image scansScanner model: IMAGE SCIENCE PATCHWORK DENSITOMETER

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Processing

SoftwareName: ERNA-3D / Classification: refinement
EM softwareName: IMAGIC / Version: 5 / Category: CTF correction
Particle selectionNum. of particles selected: 16000 / Details: from seven micrographs
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: 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 ...Details: 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.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11CSV11CSV1PDBexperimental model
21CSX11CSX2PDBexperimental model
RefinementHighest resolution: 7.5 Å / Details: CRYO-EM RECONSTRUCTION
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 62348 0 0 62348

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