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

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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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: https://doi.org/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. 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.

  • Organizational Affiliation

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


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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
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 
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Explore Q9X6J6 
Go to UniProtKB:  Q9X6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6J6
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
(GAGUU)10GAG 53-NUCLEOTIDE RNA55synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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]
C11 H12 N2 O2
Experimental Data & Validation

Experimental Data

  • 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
DENZOdata reduction
SCALEPACKdata 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: 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
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Refinement description