9KMA | pdb_00009kma

Crystal structure of the CCA-adding enzyme from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb9KMA/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-15 Released: 2025-06-18 
• Deposition Author(s): Wang, X., Li, Y.Y., Dou, Z.Y., Liu, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 
  0.294 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the CCA-adding enzyme from Arabidopsis thaliana .

Wang, X., Li, Y.Y., Dou, Z.Y., Wang, J., Liu, L.

(2025) J Struct Biol X 11: 100127-100127

• PubMed: 40519583 
• DOI: https://doi.org/10.1016/j.yjsbx.2025.100127
• Primary Citation Related Structures: 
  9KMA


• PubMed Abstract: 
  

  The 3'-terminal CCA-end of tRNA is essential for the attachment of amino acids and correct positioning of the aminoacyl-tRNA in the ribosome. In higher plants, the CCA sequence is synthesized, maintained, and repaired by class-II CCA-adding enzymes encoded by a single nuclear gene but multi-targeted to the nucleus, cytoplasm, plastids, and mitochondria. The structure of plant class-II CCA-adding enzyme remains unsolved. Here we describe the crystal structure of CCA-adding enzyme from Arabidopsis thaliana ( At CCA) . The overall structure of At CCA is similar to other class-II CCA-adding enzymes , but significant differences occur in the body domain. Structural comparison of body and tail domains between At CCA and other class-II CCA-adding enzymes unravels three specific regions of At CCA. Based on the modeled At CCA-tRNA complex, At CCA may have a different tRNA binding pattern. The three specific regions located in the body domain of At CCA also provide candidate regions for multi-targeted sorting.

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Organizational Affiliation: 
• School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 66.1 kDa 
• Atom Count: 4,065 
• Modeled Residue Count: 517 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polynucleotide adenylyltransferase family protein	A	580	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At1g22660, T22J18.17, T22J18_17
UniProt
Find proteins for A0A1P8AU61 (Arabidopsis thaliana) Explore A0A1P8AU61  Go to UniProtKB:  A0A1P8AU61

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free:  0.294 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.68	α = 90
b = 63.906	β = 90
c = 152.523	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Wang, X., Li, Y.Y., Dou, Z.Y., Liu, L.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Database references