9L8F | pdb_00009l8f

Crystal structure of RhoBAST aptamer in complex with TMR

• PDB DOI: https://doi.org/10.2210/pdb9L8F/pdb

• Classification: RNA
• Organism(s): synthetic construct
• Expression System: in vitro transcription vector pT7-TP(deltai)
• Mutation(s): No 


• Deposited: 2024-12-27 Released: 2026-07-01 
• Deposition Author(s): Tai, X.Q., Ren, A.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.231 (Depositor) 

wwPDB Validation

Currently 9L8F does not have a validation slider image.

Literature

Crystal structure of RhoBAST aptamer in complex with TMR

Tai, X.Q., Ren, A.M.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.59 kDa 
• Atom Count: 1,282 
• Modeled Residue Count: 57 
• Deposited Residue Count: 57 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (57-MER)	A [auth U]	57	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EI4( Subject of Investigation/LOI)	I [auth U]	[9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C24 H23 N2 O3 ABZLKHKQJHEPAX-UHFFFAOYSA-O
SE	B [auth U], C [auth U], D [auth U], E [auth U], F [auth U], G [auth U], H [auth U]	SELENIUM ATOM Se SPVXKVOXSXTJOY-UHFFFAOYSA-N
MG	J [auth U], K [auth U], L [auth U]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.462	α = 90
b = 84.462	β = 90
c = 107.316	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Currently 9L8F does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
Deposition Author(s): Tai, X.Q., Ren, A.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-07-01
  Type: Initial release