1YFG

YEAST INITIATOR TRNA

• PDB DOI: https://doi.org/10.2210/pdb1YFG/pdb
• NAKB: 1YFG

• Classification: T-RNA
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1997-05-08 Released: 1997-09-03 
• Deposition Author(s): Basavappa, R., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å

Starting Model: experimental

Literature

The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination.

Basavappa, R., Sigler, P.B.

(1991) EMBO J 10: 3105-3111

• PubMed: 1915284 
• DOI: https://doi.org/10.1002/j.1460-2075.1991.tb07864.x
• Primary Citation of Related Structures:  
  1YFG


• PubMed Abstract: 
  

  A significantly improved molecular model of yeast initiator tRNA (ytRNA(iMet) has been prepared that gives insight into the structural basis of eukaryotic initiator tRNA's unique function. This study was made possible by X-ray data collected at synchrotron radiation sources with the newly developed technologies of 'imaging plates' and 'storage phosphors'. These data extend beyond the resolution limit of 4.0 A reported previously to a current limit of 3.0 A and are considerably more accurate. Refinement of the model against the new data (R factor = 21.5%) clearly reveals a novel modification and a set of tertiary interactions involving sequence features characteristic of eukaryotic initiator tRNAs. We hypothesize these to be the structural elements responsible for part of the special function of yeast tRNA(iMET).

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Chicago.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.71 kDa 
• Atom Count: 1,639 
• Modelled Residue Count: 75 
• Deposited Residue Count: 75 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
YEAST INITIATOR TRNA	A	75	Saccharomyces cerevisiae

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.72	α = 90
b = 113.72	β = 90
c = 136.541	γ = 120

Software Package:

Software Name	Purpose
PHARE	model building
DENMOD	model building
NUCLIN/PROFFT	refinement
MODIFIED	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
NUCLIN	refinement
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-03 
Deposition Author(s): Basavappa, R., Sigler, P.B.

Revision History  

• Version 1.0: 1997-09-03
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description