1FIR

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 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

  • DOI: 10.1017/s1355838200000911
  • Primary Citation of Related Structures:  
    1FIR

  • 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 unambiguously shows a canonical anticodon loop ...

    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: 
    • Molecular blocs in tRNAs that could prevent +1 frameshifting
      Benas, P., Dumas, P.
      (2000) To be published --: --
    • Studies on the ternary initiation complex of HIV-1 reverse transcription and crystallographic structures of two partners
      Benas, P.
      (2000) Thesis --: 1
    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 nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)A 76Bos taurus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.72α = 90
b = 100.72β = 90
c = 82.61γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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  (Full details and data files)

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