1YFG

YEAST INITIATOR TRNA

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


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

  • 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).

    • Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, University of Chicago.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
YEAST INITIATOR TRNA75Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
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 = 113.72α = 90
b = 113.72β = 90
c = 136.541γ = 120
Software Package:
Software NamePurpose
PHAREmodel building
DENMODmodel building
NUCLIN/PROFFTrefinement
MODIFIEDrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
NUCLINrefinement
PROFFTrefinement

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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