9KBR | pdb_00009kbr

Crystal structure of the methyltransferase-ribozyme 1 bound to DNA substrate (with 1-methyl-adenosine)

• PDB DOI: https://doi.org/10.2210/pdb9KBR/pdb
• NAKB: 9KBR

• Classification: DNA-RNA HYBRID
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-10-31 Released: 2025-09-17 
• Deposition Author(s): He, Y., Yan, K., Lilley, D.M.J., Huang, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.223 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the methyltransferase ribozyme MTR1 bound to DNA substrate

He, Y., Yan, K., Lilley, D.M.J., Huang, L.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 19.9 kDa 
• Atom Count: 1,317 
• Modeled Residue Count: 62 
• Deposited Residue Count: 62 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*CP*TP*GP*(MA7)P*GP*AP*GP*CP*TP*TP*C)-3')	A	14	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')	B	24	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')	C	24	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GUN (Subject of Investigation/LOI)	E [auth C]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
NA	D [auth B], F [auth C], G [auth C], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.223 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.196	α = 90
b = 69.196	β = 90
c = 65.597	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): He, Y., Yan, K., Lilley, D.M.J., Huang, L.

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

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release