1H7M

Ribosomal Protein L30e from Thermococcus celer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Ribosomal Protein L30E from the Extreme Thermophile Thermocccus Celer: Thermal Stability and RNA Binding

Chen, Y.W.Bycroft, M.Wong, K.B.

(2003) Biochemistry 42: 2857

  • DOI: 10.1021/bi027131s
  • Also Cited By: 1W3E

  • PubMed Abstract: 
  • We report here the high-resolution crystal structure of the ribosomal protein L30e from the hyperthermophilic archaeon Thermococcus celer determined at cryo-temperature. When it is compared with its mesophilic homologue, L30e from yeast, a number of ...

    We report here the high-resolution crystal structure of the ribosomal protein L30e from the hyperthermophilic archaeon Thermococcus celer determined at cryo-temperature. When it is compared with its mesophilic homologue, L30e from yeast, a number of structural features that can enhance thermostability are revealed. Disordered residues corresponding to a large RNA-binding loop in yeast L30e are well structured in the T. celer protein. The overall charge of T. celer L30e is near neutral, whereas that of the yeast homologue is highly positive. This is the result of an increase in the number of acidic residues at the expense of polar residues, Asn, Ser, and Thr. Extensive ion pair networks are found on the molecular surface. Exposed nonpolar surface areas are reduced in the T. celer protein. Its side chain atoms preferably form hydrogen bonds with main chain atoms. Taken together, these factors contribute to high protein stability. The roles of well-conserved L30e residues are studied and found to be important in defining a very compact overall structure and in maintaining the structure of the RNA binding site. By comparing it with the yeast homologue, we also identified the residues that are responsible for RNA binding and built a model to illustrate how L30e binds to an RNA kink turn motif.


    Related Citations: 
    • Local Folding Coupled to RNA Binding in the Yeast Ribosomal Protein L30
      Mao, H.,Willamson, J.R.
      (1999) J.Mol.Biol. 292: 345
    • The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution
      Ban, N.,Nissen, P.,Hansen, J.,Moore, P.B.,Steitz, T.A.
      (2000) Science 289: 905
    • Crystallization and Preliminary Crystallographic Studies of a Ribosomal Protein L30E from the Hyperthermophilic Archaeon Thermococcus Celer
      Wong, K.B.,Wang, W.K.,Proctor, M.R.,Bycroft, M.,Chen, Y.W.
      (2001) Acta Crystallogr.,Sect.D D57: 865
    • A Novel Loop-Loop Recognition Motif in the Yeast Ribosomal Protein L30 Autoregulatory RNA Complex
      Mao, H.,White, S.A.,Willamson, J.R.
      (1999) Nat.Struct.Mol.Biol. 6: 1139


    Organizational Affiliation

    Cambridge University Chemical Laboratory and Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30E
A
102Thermococcus celerGene Names: rpl30e (rpl30)
Find proteins for P29160 (Thermococcus celer)
Go to UniProtKB:  P29160
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.165 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 48.320α = 90.00
b = 48.320β = 90.00
c = 86.420γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-07-09 
  • Released Date: 2003-04-04 
  • Deposition Author(s): Chen, Y.W., Wong, K.B.

Revision History 

  • Version 1.0: 2003-04-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Source and taxonomy