Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C11  (3D View)
Global Stoichiometry: Homo 11-mer - A11 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C11  (3D View)
Global Stoichiometry: Homo 11-mer - A11 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 204.06 kDa 
• Atom Count: 14607 
• Modelled Residue Count: 1571 
• Deposited Residue Count: 1683 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1GTF

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

• DOI: 10.2210/pdb1GTF/pdb
• BMRB: 5403
• NDB: PR0071

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Geobacillus stearothermophilus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-01-15 Released: 2002-04-05 
• Deposition Author(s): Hopcroft, N.H., Wendt, A.L., Gollnick, P., Antson, A.A.

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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 

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

• PubMed: 11914485 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	74	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: mtrB
UniProt
Find proteins for Q9X6J6 (Geobacillus stearothermophilus) Explore Q9X6J6  Go to UniProtKB:  Q9X6J6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
(GAGUU)10GAG 53-NUCLEOTIDE RNA	W	55	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP (Subject of Investigation/LOI)	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

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 = 142.077	α = 90
b = 111.493	β = 117.28
c = 138.232	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-15 
• Released Date: 2002-04-05 
Deposition Author(s): Hopcroft, N.H., Wendt, A.L., Gollnick, P., Antson, A.A.

Revision History  

• 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