1KUQ

CRYSTAL STRUCTURE OF T3C MUTANT S15 RIBOSOMAL PROTEIN IN COMPLEX WITH 16S RRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA.

Revtovich, S.V.Nikulin, A.D.Nikonov, S.V.

(2004) Biochemistry (Mosc) 69: 1319-1323

  • DOI: 10.1007/s10541-005-0076-5
  • Primary Citation of Related Structures:  
    1KUQ

  • PubMed Abstract: 
  • The position and conformation of the N-terminal helix of free ribosomal protein S15 was earlier found to be modified under various conditions. This variability was supposed to provide the recognition by the protein of its specific site on 16S rRNA. To test this hypothesis, we substituted some amino acid residues in this helix and assessed effects of these substitutions on the affinity of the protein for 16S rRNA ...

    The position and conformation of the N-terminal helix of free ribosomal protein S15 was earlier found to be modified under various conditions. This variability was supposed to provide the recognition by the protein of its specific site on 16S rRNA. To test this hypothesis, we substituted some amino acid residues in this helix and assessed effects of these substitutions on the affinity of the protein for 16S rRNA. The crystal structure of the complex of one of these mutants (Thr3Cys S15) with the 16S rRNA fragment was determined, and a computer model of the complex containing another mutant (Gln8Met S15) was designed. The available and new information was analyzed in detail, and the N-terminal helix was concluded to play no significant role in the specific binding of the S15 protein to its target on 16S rRNA.


    Related Citations: 
    • Crystal structure of the S15-rRNA complex
      Nikulin, A., Serganov, A., Ennifar, E., Tishchenko, S., Nevskaya, N., Shepard, W., Portier, C., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S., Dumas, P.
      (2000) Nat Struct Biol 7: 273

    Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15B [auth A]87Thermus thermophilusMutation(s): 1 
Gene Names: rpsOrps15
UniProt
Find proteins for P80378 (Thermus thermophilus)
Explore P80378 
Go to UniProtKB:  P80378
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNA FRAGMENTA [auth B]57Thermus thermophilus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.229α = 90
b = 128.229β = 90
c = 64.951γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance