4RVZ

Crystal structure of tRNA fluorescent labeling enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A covalent approach for site-specific RNA labeling in Mammalian cells.

Li, F.Dong, J.Hu, X.Gong, W.Li, J.Shen, J.Tian, H.Wang, J.

(2015) Angew Chem Int Ed Engl 54: 4597-4602

  • DOI: 10.1002/anie.201410433
  • Primary Citation of Related Structures:  
    4RVZ

  • PubMed Abstract: 
  • Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped ...

    Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported for the site- and sequence-specific covalent labeling of RNAs in mammalian cells by using tRNA(Ile2) -agmatidine synthetase (Tias) and click chemistry. The crystal structure of Tias in complex with an azide-bearing agmatine analogue was solved to unravel the structural basis for Tias/substrate recognition. The unique RNA sequence specificity and plastic Tias/substrate recognition enable the site-specific transfer of azide/alkyne groups to an RNA molecule of interest in vitro and in mammalian cells. Subsequent click chemistry reactions facilitate the versatile labeling, functionalization, and visualization of target RNA.


    Organizational Affiliation

    Laboratory of RNA Biology and Laboratory of Quantum Biophysics, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101 (China).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA(Ile2) 2-agmatinylcytidine synthetase TiaSA [auth Z]420Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: tiaSAF_2259
EC: 6.3.4.22
UniProt
Find proteins for O28025 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28025 
Go to UniProtKB:  O28025
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
C [auth Z]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
ZNN (Subject of Investigation/LOI)
Query on ZNN

Download Ideal Coordinates CCD File 
F [auth Z]N-(4-aminobutyl)-2-azidoacetamide
C6 H13 N5 O
SISZTIABCFMEIA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth Z]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth Z], E [auth Z]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A [auth Z]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.623α = 90
b = 69.623β = 90
c = 211.269γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MLPHAREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references