487D

SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1006/jmbi.2000.3635
  • Primary Citation of Related Structures:  

  • 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 reso ...

    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.


    Related Citations: 
    • Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin.
      Golden, B.L.,Ramakrishnan, V.,White, S.W.
      (1993) Embo J. 12: 4901
    • The Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus.
      Davies, C.,White, S.W.,Ramakrishnan, V.
      (1996) Structure 4: 55
    • The Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome.
      Nakagawa, A.,Nakashima, T.,Taniguchi, M.,Hosaka, H.,Kimura, M.,Tanaka, I.
      (1999) Embo J. 18: 1459
    • 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
    • Ribosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy.
      Hoffman, D.W.,Cameron, C.S.,Davies, C.,White, S.W.,Ramakrishnan, V.
      (1996) J.Mol.Biol. 264: 1058
    • A Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution.
      Wimberly, B.T.,Guymon, R.,Mc Cutcheon, J.P.,White, S.,Ramakrishnan, V.
      (1999) Cell 97: 491
    • The NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition.
      Stoldt, M.,Woehnert, J.,Ohlenschlaeger, O.,Goerlach, M.,Brown, L.R.
      (1999) Embo J. 18: 6508
    • Crystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus.
      Nikonov, S.,Nevskaya, N.,Eliseikina, I.,Fomenkova, N.,Nikulin, A.,Ossina, N.,Garber, M.,Jonsson, B.H.,Briand, C.,Al-Karadaghi, S.,Svensson, A.,Aevarsson, A.,Liljas, A.
      (1996) Embo J. 15: 1350


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L1 RIBOSOMAL PROTEIN)
H
224Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L2 RIBOSOMAL PROTEIN)
I
135Geobacillus stearothermophilusMutation(s): 3 
Gene Names: rplB
Find proteins for P04257 (Geobacillus stearothermophilus)
Go to UniProtKB:  P04257
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L6 RIBOSOMAL PROTEIN)
J
164Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rplF
Find proteins for P02391 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02391
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L9 RIBOSOMAL PROTEIN)
K
149Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rplI
Find proteins for P02417 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02417
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L11 RIBOSOMAL PROTEIN)
L
133Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L14 RIBOSOMAL PROTEIN)
M
122Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rplN
Find proteins for P04450 (Geobacillus stearothermophilus)
Go to UniProtKB:  P04450
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (50S L25 RIBOSOMAL PROTEIN)
N
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH2
Query on NH2

Download SDF File 
Download CCD File 
N
AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
N
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
I
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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: Version format compliance