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: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.230 

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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
  • Primary Citation of Related Structures:  
    1C9S

  • 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 two or three non-conserved nucleotides ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRP RNA-BINDING ATTENUATION PROTEIN74Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mtrB
UniProt
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Explore Q9X6J6 
Go to UniProtKB:  Q9X6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6J6
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SINGLE STRANDED RNA (55-MER)A [auth W]55N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth D],
CA [auth E],
DA [auth F],
EA [auth G],
AA [auth C],
BA [auth D],
CA [auth E],
DA [auth F],
EA [auth G],
FA [auth H],
GA [auth I],
HA [auth J],
IA [auth K],
JA [auth L],
KA [auth M],
LA [auth N],
MA [auth O],
NA [auth P],
OA [auth Q],
PA [auth R],
QA [auth S],
RA [auth T],
SA [auth U],
TA [auth V],
X [auth A],
Y [auth A],
Z [auth B]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.97α = 90
b = 111.67β = 117.77
c = 138.68γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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