1DV4

PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site.

Tocilj, A.Schlunzen, F.Janell, D.Gluhmann, M.Hansen, H.A.Harms, J.Bashan, A.Bartels, H.Agmon, I.Franceschi, F.Yonath, A.

(1999) Proc.Natl.Acad.Sci.USA 96: 14252-14257


  • PubMed Abstract: 
  • The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 A resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins ...

    The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 A resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.


    Related Citations: 
    • The structure of ribosomal protein S7 at 1.9 angstrom resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids
      Wimberly, B.T.,White, S.,Ramakrishnan, V.
      (1997) Structure 5: 1187
    • The structure of ribosomal protein-S5 reveals sites of interaction with 16S ribosomal-RNA
      Ramakrishnan, V.,White, S.
      (1992) Nature 358: 768
    • The structure of the 9(18)-heteropoly anion in potassium 9(18)-tungstophosphate, K6(P2W18O62).14H2O
      Dawson, B.
      (1953) Acta Crystallogr. 6: 113


    Organizational Affiliation

    Max Planck Research Unit for Ribosomal Structure, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S5
E
145Geobacillus stearothermophilusGene Names: rpsE
Find proteins for P02357 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02357
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S7
G
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 1
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNAA362Thermus thermophilus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO2
Query on WO2

Download SDF File 
Download CCD File 
E
OCTADECATUNGSTENYL DIPHOSPHATE
O62 P2 W18
WXCYUHHUPKCTBX-HWHNUBGVCD
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
N
Query on N
A
RNA LINKINGC5 H11 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 407.100α = 90.00
b = 407.100β = 90.00
c = 176.008γ = 90.00
Software Package:
Software NamePurpose
Omodel building
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description