3AEV

Crystal structure of a/eIF2alpha-aDim2p-rRNA complex from Pyrococcus horikoshii OT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA

Jia, M.Z.Horita, S.Nagata, K.Tanokura, M.

(2010) J.Mol.Biol. 398: 774-785

  • DOI: 10.1016/j.jmb.2010.03.055

  • PubMed Abstract: 
  • Dim2p is a eukaryal small ribosomal subunit RNA processing factor required for the maturation of 18S rRNA. Here we show that an archaeal homolog of Dim2p, aDim2p, forms a ternary complex with the archaeal homolog of eIF2 alpha, a/eIF2 alpha, and the ...

    Dim2p is a eukaryal small ribosomal subunit RNA processing factor required for the maturation of 18S rRNA. Here we show that an archaeal homolog of Dim2p, aDim2p, forms a ternary complex with the archaeal homolog of eIF2 alpha, a/eIF2 alpha, and the RNA fragment that possesses the 3' end sequence of 16S rRNA both in solution and in crystal. The 2.8-A crystal structure of the ternary complex reveals that two KH domains of aDim2p, KH-1 and -2, are involved in binding the anti-Shine-Dalgarno core sequence (CCUCC-3') and a highly conserved adjacent sequence (5'-GGAUCA), respectively, of the target rRNA fragment. The surface plasmon resonance results show that the interaction of aDim2p with the target rRNA fragment is very strong, with a dissociation constant of 9.8 x 10(-10) M, and that aDim2p has a strong nucleotide sequence preference for the 3' end sequence of 16S rRNA. On the other hand, aDim2p interacts with the isolated alpha subunit and the intact alpha beta gamma complex of a/eIF2, irrespective of the RNA binding. These results suggest that aDim2p is a possible archaeal pre-rRNA processing factor recognizing the 3' end sequence (5'-GAUCACCUCC-3') of 16S rRNA and may have multiple biological roles in vivo by interacting with other proteins such as a/eIF2 and aRio2p.


    Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit alpha
A
275Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: eif2a
Find proteins for O58655 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O58655
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein PH1566
B
219Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Find proteins for O59282 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59282
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*AP*UP*CP*AP*CP*CP*UP*CP*C)-3')C11N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.998α = 90.00
b = 93.600β = 90.00
c = 116.704γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-01-29
    Type: Database references