6ZPF

Racemic compound of RNA duplexes.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Broken symmetry between RNA enantiomers in a crystal lattice.

Kiliszek, A.Blaszczyk, L.Bejger, M.Rypniewski, W.

(2021) Nucleic Acids Res 49: 12535-12539

  • DOI: https://doi.org/10.1093/nar/gkab480
  • Primary Citation of Related Structures:  
    6ZPF, 6ZQ9, 6ZR1, 6ZRL, 6ZRS, 6ZW3, 6ZWU, 6ZX5, 6ZX8, 7A9L, 7A9N, 7A9O, 7A9P, 7A9Q, 7A9R, 7A9S, 7A9T

  • PubMed Abstract: 

    Explaining the origin of the homochirality of biological molecules requires a mechanism of disrupting the natural equilibrium between enantiomers and amplifying the initial imbalance to significant levels. Authors of existing models have sought an explanation in the parity-breaking weak nuclear force, in some selectively acting external factor, or in random fluctuations that subsequently became amplified by an autocatalytic process. We have obtained crystals in which l- and d-enantiomers of short RNA duplexes assemble in an asymmetric manner. These enantiomers make different lattice contacts and have different exposures to water and metal ions present in the crystal. Apparently, asymmetry between enantiomers can arise upon their mutual interactions and then propagate via crystallization. Asymmetric racemic compounds are worth considering as possible factors in symmetry breaking and enantioenrichment that took place in the early biosphere.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')A [auth K]8Thermus thermophilus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')B [auth L]8Thermus thermophilus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')C [auth M]8Thermus thermophilus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')D [auth N]8Thermus thermophilus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.85α = 106.107
b = 26.5β = 96.001
c = 38.57γ = 92.722
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 2.0: 2023-07-26
    Changes: Derived calculations, Polymer sequence
  • Version 2.1: 2024-01-31
    Changes: Data collection, Refinement description