1FIR

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop.

Benas, P., Bec, G., Keith, G., Marquet, R., Ehresmann, C., Ehresmann, B., Dumas, P.

(2000) RNA 6: 1347-1355


  • PubMed Abstract: 

    • We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambig ...

    We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambiguously shows a canonical anticodon loop. This contradicts previous results in short RNA fragment studies and leads us to conclude that neither frameshifting specificities of tRNA(Lys) nor tRNA(Lys,3) primer selection by HIV are due to a specific three-dimensional anticodon structure. Comparison of our structure with the results of an NMR study on a hairpin representing a nonmodified anticodon stem-loop makes plausible the conclusion that chemical modifications of the wobble base U34 to 5-methoxycarbonyl-methyl-2-thiouridine and of A37 to 2-methylthio-N-6-threonylcarbamoyl-adenosine would be responsible for a canonical 7-nt anticodon-loop structure, whereas the unmodified form would result in a noncanonical UUU short triloop. The hexagonal crystal packing is remarkable and shows tight dimers of tRNAs forming a right-handed double superhelix. Within the dimers, the tRNAs are associated head-to-tail such that the CCA end of one tRNA interacts with the anticodon of the symmetry-related tRNA. This provides us with a partial view of a codon-anticodon interaction and gives insights into the positioning of residue 37, and of its posttranscriptional modifications, relative to the first base of the codon.

    Related Citations: 
    • Studies on the ternary initiation complex of HIV-1 reverse transcription and crystallographic structures of two partners
      Benas, P.
      (2000) Thesis --: 1
    • Molecular blocs in tRNAs that could prevent +1 frameshifting
      Benas, P.,Dumas, P.
      (2000) TO BE PUBLISHED --: --

    Organizational Affiliation: 

    Unité Propre de Recherche 9002 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)A76Bos taurus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
12A
Query on 12A
A
RNA LINKINGC16 H23 N6 O11 P SA
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
1MA
Query on 1MA
A
RNA LINKINGC11 H16 N5 O7 PA
70U
Query on 70U
A
RNA LINKINGC12 H17 N2 O10 P SU
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A
RNA LINKINGC11 H18 N5 O8 PG
2MU
Query on 2MU
A
RNA LINKINGC11 H17 N2 O9 PU
H2U
Query on H2U
A
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 100.720α = 90.00
b = 100.720β = 90.00
c = 82.610γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2000-08-06 
  • Released Date: 2001-01-17 
  • Deposition Author(s): Benas, P., Dumas, P.

Revision History 

  • Version 1.0: 2001-01-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2014-04-09
    Type: Derived calculations
  • Version 1.4: 2018-04-04
    Type: Data collection
  • Version 1.5: 2018-04-11
    Type: Data collection