7EOJ

Crystal structure of the Pepper aptamer in complex with HBC, cesium soak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


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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 

  • DOI: 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 ...

    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. aimingren@zju.edu.cn.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Pepper (49-MER)A49synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J8F
Query on J8F

Download Ideal Coordinates CCD File 
B [auth A]4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile
C19 H17 N3 O
DIAVZHWDYXQAFC-LDADJPATSA-N
 Ligand Interaction
CS (Subject of Investigation/LOI)
Query on CS

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.277α = 90
b = 34.749β = 127.93
c = 58.124γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-04-22 
  • Released Date: 2021-11-24 
  • Deposition Author(s): Huang, K.Y., Ren, A.M.

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