1GTF

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 53-nucleotide RNA molecule containing GAGUU repeats

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Specificity of Trap-RNA Interactions: Crystal Structures of Two Complexes with Different RNA Sequences

Hopcroft, N.H., Wendt, A.L., Gollnick, P., Antson, A.A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 615

  • DOI: 10.1107/s0907444902003189
  • Primary Citation of Related Structures:  
    1GTF, 1GTN

  • PubMed Abstract: 

    • The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in bacilli by binding to the leader region of the nascent trp operon mRNA. When activated by binding tryptophan, the 11-subunit circular TRAP molecule binds to a target sequence consisting of 11 (G/U)AG repeats, separated by two or three variable 'spacer' nucleotides ...

    The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in bacilli by binding to the leader region of the nascent trp operon mRNA. When activated by binding tryptophan, the 11-subunit circular TRAP molecule binds to a target sequence consisting of 11 (G/U)AG repeats, separated by two or three variable 'spacer' nucleotides. Reported here are two crystal structures of TRAP bound to RNAs containing 11 GAG repeats separated by UU and CC spacer nucleotides, determined at 1.75 and 2.50 A resolution, respectively. These show the spacer regions of the RNA molecules to be highly flexible, making no direct hydrogen-bonding contacts with the protein. Comparison of these structures with the previous structure of TRAP bound to (GAGAU)(10)GAG RNA, in which the spacer nucleotides stack with each other close to the protein surface, shows that the RNA can adopt different conformations depending on the sequence of the spacer regions. This gives insight into the structural basis of the specificity of TRAP and into the mechanism of binding.

    Related Citations: 
    • Structure of the Trp RNA-Binding Attenuation Protein, Trap, Bound to RNA
      Antson, A.A., Dodson, E.J., Dodson, G.G., Greaves, R.B., Chen, X.-P., Gollnick, P.
      (1999) Nature 401: 235
    Organizational Affiliation: 

    York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRP RNA-BINDING ATTENUATION PROTEIN (TRAP)
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
74Geobacillus 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
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
(GAGUU)10GAG 53-NUCLEOTIDE RNAW 55synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP
Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth G],
EA [auth H],
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth G],
EA [auth H],
FA [auth I],
GA [auth J],
HA [auth K],
IA [auth L],
JA [auth M],
KA [auth N],
LA [auth O],
MA [auth P],
NA [auth Q],
OA [auth R],
PA [auth S],
QA [auth T],
RA [auth U],
SA [auth V],
X [auth A],
Y [auth B],
Z [auth C]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.077α = 90
b = 111.493β = 117.28
c = 138.232γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Changes: Advisory, Derived calculations, Other, Source and taxonomy