1FEU

CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TL5, ONE OF THE CTC FAMILY PROTEINS, COMPLEXED WITH A FRAGMENT OF 5S RRNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.

Fedorov, R.Meshcheryakov, V.Gongadze, G.Fomenkova, N.Nevskaya, N.Selmer, M.Laurberg, M.Kristensen, O.Al-Karadaghi, S.Liljas, A.Garber, M.Nikonov, S.

(2001) Acta Crystallogr.,Sect.D 57: 968-976


  • PubMed Abstract: 
  • The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 A resolution. The protein consists of two domains. The structure of the N-terminal domain is close t ...

    The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 A resolution. The protein consists of two domains. The structure of the N-terminal domain is close to the structure of E. coli ribosomal protein L25, but the C-terminal domain represents a new fold composed of seven beta-strands connected by long loops. TL5 binds to the RNA through its N-terminal domain, whereas the C-terminal domain is not included in this interaction. Cd(2+) ions, the presence of which improved the crystal quality significantly, bind only to the protein component of the complex and stabilize the protein molecule itself and the interactions between the two molecules in the asymmetric unit of the crystal. The TL5 sequence reveals homology to the so-called general stress protein CTC. The hydrophobic cores which stabilize both TL5 domains are highly conserved in CTC proteins. Thus, all CTC proteins may fold with a topology close to that of TL5.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
A, D
206Thermus thermophilusGene Names: rplY (rpl25, rptL5)
Find proteins for P56930 (Thermus thermophilus)
Go to UniProtKB:  P56930
Entity ID: 1
MoleculeChainsLengthOrganism
19 NT FRAGMENT OF 5S RRNAB,E19N/A
Entity ID: 2
MoleculeChainsLengthOrganism
21 NT FRAGMENT OF 5S RRNAC,F21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 109.904α = 90.00
b = 109.904β = 90.00
c = 137.511γ = 120.00
Software Package:
Software NamePurpose
DMmodel building
MAR345data collection
SCALEPACKdata scaling
DMphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-25
    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: Data collection, Refinement description