Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.8 kDa 
• Atom Count: 3,519 
• Modelled Residue Count: 319 
• Deposited Residue Count: 448 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1P6V

Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB

• PDB DOI:  https://doi.org/10.2210/pdb1P6V/pdb
• NDB: PR0098

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-04-30 Released: 2003-08-12 
• Deposition Author(s): Gutmann, S., Haebel, P.W., Metzinger, L., Sutter, M., Felden, B., Ban, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.360 
• R-Value Work: 0.302 
• R-Value Observed: 0.302 

Literature

Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB

Gutmann, S., Haebel, P.W., Metzinger, L., Sutter, M., Felden, B., Ban, N.

(2003) Nature 424: 699-703

• PubMed: 12904796 
• DOI: https://doi.org/10.1038/nature01831
• Primary Citation of Related Structures:  
  1P6V


• PubMed Abstract: 
  

Accurate translation of genetic information into protein sequence depends on complete messenger RNA molecules. Truncated mRNAs cause synthesis of defective proteins, and arrest ribosomes at the end of their incomplete message. In bacteria, a hybrid RNA molecule that combines the functions of both transfer and messenger RNAs (called tmRNA) rescues stalled ribosomes, and targets aberrant, partially synthesized, proteins for proteolytic degradation. Here we report the 3.2-A-resolution structure of the tRNA-like domain of tmRNA (tmRNA(Delta)) in complex with small protein B (SmpB), a protein essential for biological functions of tmRNA. We find that the flexible RNA molecule adopts an open L-shaped conformation and SmpB binds to its elbow region, stabilizing the single-stranded D-loop in an extended conformation. The most striking feature of the structure of tmRNA(Delta) is a 90 degrees rotation of the TPsiC-arm around the helical axis. Owing to this unusual conformation, the SmpB-tmRNA(Delta) complex positioned into the A-site of the ribosome orients SmpB towards the small ribosomal subunit, and directs tmRNA towards the elongation-factor binding region of the ribosome. On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome.

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Organizational Affiliation: 

Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg (ETH Zürich), HPK Gebäude, CH-8093 Zürich, Switzerland.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SsrA-binding protein	C [auth A], D [auth C]	156	Aquifex aeolicus	Mutation(s): 0  Gene Names: smpB
UniProt
Find proteins for O66640 (Aquifex aeolicus (strain VF5)) Explore O66640  Go to UniProtKB:  O66640

Entity ID: 1
Molecule	Chains	Length	Organism	Image
45-MER	A [auth B], B [auth D]	68	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.360 
• R-Value Work: 0.302 
• R-Value Observed: 0.302 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.68	α = 90
b = 99.68	β = 90
c = 207.05	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-12 
Deposition Author(s): Gutmann, S., Haebel, P.W., Metzinger, L., Sutter, M., Felden, B., Ban, N.

Revision History  

• Version 1.0: 2003-08-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance