4TRA

RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS


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

Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.

Westhof, E.Dumas, P.Moras, D.

(1988) Acta Crystallogr.,Sect.A 44: 112-123

  • Primary Citation of Related Structures:  2TRA, 3TRA

  • PubMed Abstract: 
  • Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% fo ...

    Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% for about 4500 reflections between 10 and 3 A. In yeast tRNA(Asp) crystals the molecules exist as dimers with base pairings of the anticodon (AC) triplets and labilization of the tertiary interaction between one invariant guanine of the dihydrouridine (D) loop and the invariant cytosine of the thymine (T) loop (G19-C56). In yeast tRNA(Phe) crystals, the molecules exist as monomers with only weak intermolecular packing contacts between symmetry-related molecules. Despite this, the tertiary folds of the L-shaped tRNA structures are identical when allowance is made for base sequence changes between tRNA(Phe) and tRNA(Asp). However, the relative mobilities of two regions are inverse in the two structures with the AC loop more mobile than the D loop in tRNA(Phe) and the D loop more mobile than the AC loop in tRNA(Asp). In addition, the T loop becomes mobile in tRNA(Asp). The present refinements were performed to exclude packing effects or refinement bias as possible sources of such differential dynamic behavior. It is concluded that the transfer of flexibility from the anticodon to the D- and T-loop region in tRNA(Asp) is not a crystal-line artefact. Further, analysis of the four structures supports a mechanism for the flexibility transfer through base stacking in the AC loop and concomitant variations in twist angles between base pairs of the anticodon helix which propagate up to the D- and T-loop region.


    Related Citations: 
    • RNA-Ligand Interactions. (1) Magnesium Binding Sites in Yeast T-RNA-PHE
      Holbrook, S.R.,Sussman, J.L.,Warrant, R.W.,Church, G.M.,Kim, S.-H.
      (1977) Nucleic Acids Res. 4: 2811
    • Three-dimensional Structure of a Transfer RNA in Two Crystal Forms
      Sussman, J.L.,Kim, S.-H.
      (1976) Science 192: 853
    • Idealized Atomic Coordinates of Yeast Phenylalanine Transfer RNA
      Sussman, J.L.,Kim, S.-H.
      (1976) Biochem.Biophys.Res.Commun. 68: 89
    • Crystal Structure of Yeast Phenylalanine T-RNA. II.Structural Features and Functional Implications
      Holbrook, S.R.,Sussman, J.L.,Warrant, R.W.,Kim, S.-H.
      (1978) J.Mol.Biol. 123: 631
    • Hydration of Transfer RNA Molecules. A Crystallographic Study
      Westhof, E.,Dumas, P.,Moras, D.
      (1988) Biochimie 70: 145
    • The Three-Dimensional Structure of Transfer RNA
      Rich, A.,Kim, S.H.
      (1978) Sci.Am. 238: 52
    • Crystal Structure of Yeast Phenylalanine T-RNA, its Correlation to the Solution Structure and the Functional Implications
      Kim, S.-H.
      (1978) Transfer RNA --: --
    • Three Dimensional Structure of T-RNA and its Functional Implications
      Kim, S.-H.
      (1978) Adv.Enzymol.Relat.Areas Mol.Biol. 46: 279
    • Crystal Structure of Yeast Phenylalanine T-RNA. I.Crystallographic Refinement
      Sussman, J.L.,Holbrook, S.R.,Warrant, R.W.,Church, G.M.,Kim, S.-H.
      (1978) J.Mol.Biol. 123: 607


    Organizational Affiliation

    Institut de Biologie Mol├ęculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
TRNAPHEA76Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
A
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
A
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
A
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
A
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
A
RNA LINKINGC10 H15 N2 O9 PU
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 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 33.000α = 90.00
b = 56.000β = 90.00
c = 161.000γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1987-11-06
    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