7SZU

Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Fluorescence Activation by Pepper RNA.

Rees, H.C.Gogacz, W.Li, N.S.Koirala, D.Piccirilli, J.A.

(2022) ACS Chem Biol 17: 1866-1875

  • DOI: https://doi.org/10.1021/acschembio.2c00290
  • Primary Citation of Related Structures:  
    7SZU, 7U0Y

  • PubMed Abstract: 

    Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K + dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg 2+ ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.


  • Organizational Affiliation

    Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BL3-6 Fab heavy chainB [auth H]224Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BL3-6 Fab light chainC [auth L]213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA aptamerA [auth R]67synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.609α = 90
b = 96.992β = 90
c = 148.255γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM102489

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description