6UGG

Structure of unmodified E. coli tRNA(Asp)

  • Classification: RNA
  • Organism(s): Escherichia coli

  • Deposited: 2019-09-26 Released: 2020-01-01 
  • Deposition Author(s): Chan, C.W., Mondragon, A.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.

Chan, C.W.Badong, D.Rajan, R.Mondragon, A.

(2019) Rna --: --

  • DOI: 10.1261/rna.073478.119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies ...

    Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as prototypical folded RNA molecules. Although conformational flexibility is a well-established characteristic of tRNA structure, it is typically regarded as an adaptive property exhibited in response to an inducing event, such as the binding of a tRNA synthetase or the accommodation of an aminoacyl-tRNA into the ribosome. In this study, we present crystallographic data of a tRNA molecule to expand on this paradigm by showing that structural flexibility and plasticity are intrinsic properties of tRNAs, apparent even in the absence of other factors. Based on two closely related conformations observed within the same crystal, we posit that unbound tRNAs by themselves are flexible and dynamic molecules. Furthermore, we demonstrate that the formation of the T-loop conformation by the tRNA TΨC stem-loop, a well-characterized and classic RNA structural motif, is possible even in the absence of important interactions observed in fully folded tRNAs.


    Organizational Affiliation

    Northwestern University a-mondragon@northwestern.edu.,Northwestern University.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
tRNAaspA,B77Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.677α = 90.00
b = 64.677β = 90.00
c = 195.799γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
STARANISOdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01 GM058443
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35 GM118108
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesT32 GM008152
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesT32 GM008382

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release