9KFX | pdb_00009kfx

Crystal structure of synthetic PPR-DYW in complex with target RNA

• PDB DOI: https://doi.org/10.2210/pdb9KFX/pdb
• NAKB: 9KFX

• Classification: HYDROLASE/RNA
• Organism(s): synthetic construct, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-07 Released: 2025-11-12 
• Deposition Author(s): Teramoto, T., Okada, A., Urushihara, R., Gutmann, B., Ichinose, M., Yagi, Y., Nakamura, T., Kakuta, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.243 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Models: experimental, in silico

Literature

Structural basis of C-to-U RNA editing by PPR-DYW protein

Teramoto, T., Urushihara, R., Aoyama, R., Okada, A., Gutmann, B., Ichinose, M., Yagi, Y., Kakuta, Y., Nakamura, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 148.53 kDa 
• Atom Count: 10,444 
• Modeled Residue Count: 1,262 
• Deposited Residue Count: 1,262 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic PPR-DYW protein	A, B	612	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
rpoA RNA (5'-R(*UP*UP*AP*CP*AP*CP*GP*UP*GP*CP*AP*AP*AP*AP*UP*CP*UP*G)-3')	C [auth R], D [auth r]	18	Arabidopsis thaliana

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.243 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.66	α = 90
b = 109.35	β = 90
c = 187.41	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Teramoto, T., Okada, A., Urushihara, R., Gutmann, B., Ichinose, M., Yagi, Y., Nakamura, T., Kakuta, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 2.0: 2026-01-21
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary