7EOM

Crystal structure of the Pepper aptamer in complex with HBC508


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure-based investigation of fluorogenic Pepper aptamer.

Huang, K.Chen, X.Li, C.Song, Q.Li, H.Zhu, L.Yang, Y.Ren, A.

(2021) Nat Chem Biol 17: 1289-1295

  • DOI: https://doi.org/10.1038/s41589-021-00884-6
  • Primary Citation of Related Structures:  
    7EOG, 7EOH, 7EOI, 7EOJ, 7EOK, 7EOL, 7EOM, 7EON, 7EOO, 7EOP

  • PubMed Abstract: 

    Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.


  • Organizational Affiliation

    Life Sciences Institute, Zhejiang University, Hangzhou, China.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Pepper (49-MER)48synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.078α = 90
b = 34.874β = 127.35
c = 57.861γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Source and taxonomy
  • Version 1.2: 2022-02-16
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description