1DV4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 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 U S A 96: 14252-14257

  • DOI: 10.1073/pnas.96.25.14252
  • Primary Citation of Related Structures:  
    1DV4

  • 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. 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 ...

    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-S5 reveals sites of interaction with 16S ribosomal-RNA
      Ramakrishnan, V., White, S.
      (1992) Nature 358: 768
    • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5 E145Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rpsE
Find proteins for P02357 (Geobacillus stearothermophilus)
Explore P02357 
Go to UniProtKB:  P02357
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7 G135Thermus thermophilusMutation(s): 0 
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P17291 
Go to UniProtKB:  P17291
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA362Thermus thermophilus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO2
Query on WO2

Download Ideal Coordinates CCD File 
E
OCTADECATUNGSTENYL DIPHOSPHATE
O62 P2 W18
WXCYUHHUPKCTBX-HWHNUBGVCD
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 407.1α = 90
b = 407.1β = 90
c = 176.008γ = 90
Software Package:
Software NamePurpose
SHARPphasing
Omodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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