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 2.0 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: https://doi.org/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. 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.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5B [auth E]145Geobacillus stearothermophilusMutation(s): 0 
UniProt
Find proteins for P02357 (Geobacillus stearothermophilus)
Explore P02357 
Go to UniProtKB:  P02357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02357
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7C [auth G]135Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P17291 
Go to UniProtKB:  P17291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17291
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA362Thermus thermophilus
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WO2
Query on WO2

Download Ideal Coordinates CCD File 
D [auth E]OCTADECATUNGSTENYL DIPHOSPHATE
O62 P2 W18
WXCYUHHUPKCTBX-UHFFFAOYSA-A
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

View Full Validation Report



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
  • Version 2.0: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Polymer sequence