1C9S

CRYSTAL STRUCTURE OF A COMPLEX OF TRP RNA-BINDING ATTENUATION PROTEIN WITH A 53-BASE SINGLE STRANDED RNA CONTAINING ELEVEN GAG TRIPLETS SEPARATED BY AU DINUCLEOTIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA.

Antson, A.A.Dodson, E.J.Dodson, G.Greaves, R.B.Chen, X.Gollnick, P.

(1999) Nature 401: 235-242

  • DOI: 10.1038/45730
  • Also Cited By: 1GTF, 1GTN, 1UTD, 1UTF, 1UTV, 4V4F

  • PubMed Abstract: 
  • The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes of several bacilli by binding single-stranded RNA. The binding sequence is composed of eleven triplet repeats, predominantly GAG, separated by tw ...

    The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes of several bacilli by binding single-stranded RNA. The binding sequence is composed of eleven triplet repeats, predominantly GAG, separated by two or three non-conserved nucleotides. Here we present the crystal structure of a complex of TRAP and a 53-base single-stranded RNA containing eleven GAG triplets, revealing that each triplet is accommodated in a binding pocket formed by beta-strands. In the complex, the RNA has an extended structure without any base-pairing and binds to the protein mostly by specific protein-base interactions. Eleven binding pockets on the circular TRAP 11-mer form a belt with a diameter of about 80 A. This simple but elegant mechanism of arresting the RNA segment by encircling it around a protein disk is applicable to both transcription, when TRAP binds the nascent RNA, and to translation, when TRAP binds the same sequence within a non-coding leader region of the messenger RNA.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, UK. fred@yorvic.york.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRP RNA-BINDING ATTENUATION PROTEIN
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
74Geobacillus stearothermophilusGene Names: mtrB
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X6J6
Entity ID: 1
MoleculeChainsLengthOrganism
SINGLE STRANDED RNA (55-MER)W55N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.970α = 90.00
b = 111.670β = 117.77
c = 138.680γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance