9G4P | pdb_00009g4p

Crystal structure of the skipping-rope RNA motif.

• PDB DOI: https://doi.org/10.2210/pdb9G4P/pdb
• NAKB: 9G4P

• Classification: RNA
• Organism(s): bacterium
• Mutation(s): No 


• Deposited: 2024-07-16 Released: 2025-07-30 
• Deposition Author(s): Huang, L., Lilley, D.M.J.
• Funding Organization(s): Cancer Research UK, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.322 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Structural basis for tRNA-mimicking by skipping-rope RNA motif

Huang, L., Lilley, D.M.J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 22.13 kDa 
• Atom Count: 1,415 
• Modeled Residue Count: 66 
• Deposited Residue Count: 68 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (33-MER)	A	35	bacterium

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (33-MER)	B	33	bacterium

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.232 (Depositor), 0.322 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.478	α = 90
b = 113.478	β = 90
c = 59.286	γ = 120

Software Package:

Software Name	Purpose
xia2	data reduction
xia2	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Huang, L., Lilley, D.M.J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	A18604
National Natural Science Foundation of China (NSFC)	China	32171191

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release