1YFG

YEAST INITIATOR TRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 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


  • 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 synch ...

    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).

    Related Citations: 
    • Crystal Structure of a Eukaryotic Initiator tRNA
      Schevitz, R.W.,Podjarny, A.D.,Krishnamachari, N.,Hughes, J.J.,Sigler, P.B.,Sussman, J.L.
      (1979) Nature 278: 188

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, University of Chicago.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
YEAST INITIATOR TRNAA75Saccharomyces cerevisiae
Small Molecules
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
RIA
Query on RIA
A
RNA LINKINGC15 H23 N5 O14 P2A
1MG
Query on 1MG
A
RNA LINKINGC11 H16 N5 O8 PG
M2G
Query on M2G
A
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
A
RNA LINKINGC11 H16 N5 O7 PA
T6A
Query on T6A
A
RNA LINKINGC15 H21 N6 O11 PA
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A
RNA LINKINGC11 H18 N5 O8 PG
H2U
Query on H2U
A
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 113.720α = 90.00
b = 113.720β = 90.00
c = 136.541γ = 120.00
Software Package:
Software NamePurpose
PHAREmodel building
NUCLINrefinement
MODIFIEDrefinement
NUCLIN/PROFFTrefinement
DENMODmodel building
DMphasing
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-03
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance