7L0Z | pdb_00007l0z

Spinach variant bound to DFHBI-1T

PDB DOI: https://doi.org/10.2210/pdb7L0Z/pdb
NAKB: 7L0Z

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2020-12-13 Released: 2021-05-26
Deposition Author(s): Truong, L., Trachman, R.J., Ferre-D'Amare, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.232 (Depositor), 0.234 (DCC)
R-Value Work:
0.196 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.

Jeng, S.C.Y., Trachman III, R.J., Weissenboeck, F., Truong, L., Link, K.A., Jepsen, M.D.E., Knutson, J.R., Andersen, E.S., Ferre-D'Amare, A.R., Unrau, P.J.

(2021) RNA 27: 433-444

PubMed: 33376189 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1261/rna.078220.120
Primary Citation Related Structures:
6UP0, 7L0Z

PubMed Abstract:
To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

Organizational Affiliation

Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.

Macromolecule Content

Total Structure Weight: 23.64 kDa
Atom Count: 1,612
Modeled Residue Count: 69
Deposited Residue Count: 69
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (69-MER)	A [auth G]	69	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2ZY Query on 2ZY Download:Ideal Coordinates CCD File SDF format, chain B [auth G] MOL2 format, chain B [auth G] mmCIF format, chain B [auth G]	B [auth G]	(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one C₁₃ H₉ F₅ N₂ O₂ AWYCLBWNRONMQC-WMZJFQQLSA-N		Interactions Focus chain B [auth G] Interactions & Density Focus chain B [auth G]
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain D [auth G] SDF format, chain C [auth G] MOL2 format, chain E [auth G] MOL2 format, chain D [auth G] MOL2 format, chain C [auth G] mmCIF format, chain E [auth G] mmCIF format, chain D [auth G] mmCIF format, chain C [auth G]	C [auth G], D [auth G], E [auth G]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain C [auth G] Focus chain D [auth G] Focus chain E [auth G] Interactions & Density Focus chain C [auth G] Focus chain D [auth G] Focus chain E [auth G]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth G] SDF format, chain G MOL2 format, chain H [auth G] MOL2 format, chain G mmCIF format, chain H [auth G] mmCIF format, chain G	G, H [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G Focus chain H [auth G] Interactions & Density Focus chain G Focus chain H [auth G]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain K [auth G] MOL2 format, chain L [auth G] MOL2 format, chain K [auth G] mmCIF format, chain L [auth G] mmCIF format, chain K [auth G]	K [auth G], L [auth G]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth G] Focus chain L [auth G] Interactions & Density Focus chain K [auth G] Focus chain L [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth G] MOL2 format, chain F [auth G] mmCIF format, chain F [auth G]	F [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth G] Interactions & Density Focus chain F [auth G]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth G] SDF format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain I [auth G] mmCIF format, chain J [auth G] mmCIF format, chain I [auth G]	I [auth G], J [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth G] Focus chain J [auth G] Interactions & Density Focus chain I [auth G] Focus chain J [auth G]