2V7R | pdb_00002v7r

Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb2V7R/pdb
• NAKB: 2V7R

• Classification: RNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-08-01 Released: 2008-03-18 
• Deposition Author(s): Foerster, C., Mankowska, M., Fuerste, J.P., Perbandt, M., Betzel, C., Erdmann, V.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal Structure of a Human Trnagly Microhelix at 1.2 A Resolution.

Foerster, C., Mankowska, M., Fuerste, J.P., Perbandt, M., Betzel, C., Erdmann, V.A.

(2008) Biochem Biophys Res Commun 368: 996

• PubMed: 18279665 
• DOI: https://doi.org/10.1016/j.bbrc.2008.01.175
• Primary Citation Related Structures: 
  2V7R


• PubMed Abstract: 
  

  The tRNA(Gly)/glycyl-tRNA synthetase (GlyRS) system belongs to the so-called 'class II aminoacyl-tRNA synthetase system' in which tRNA identity elements are assured by rather few and simple determinants mostly located in the tRNA acceptor stem. Regarding evolutionary aspects, the tRNA(Gly)/GlyRS system is a special case. There exist two different types of GlyRS, namely an archaebacterial/human type and a eubacterial type reflecting an evolutionary divergence within this system. Here we report the crystal structure of a human tRNA(Gly) acceptor stem microhelix at 1.2A resolution. The local geometric parameters of the microhelix and the water network surrounding the RNA are presented. The structure complements the previously published Escherichia coli tRNA(Gly) aminoacyl stem structure.

---

Organizational Affiliation: 
• Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany.

Biological Assembly 1  

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 4.43 kDa 
• Atom Count: 378 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HUMAN TRNAGLY MICROHELIX	A	7	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
HUMAN TRNAGLY MICROHELIX	B	7	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.12	α = 90
b = 37.491	β = 113.02
c = 30.379	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Foerster, C., Mankowska, M., Fuerste, J.P., Perbandt, M., Betzel, C., Erdmann, V.A.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Other