9KMA | pdb_00009kma

Crystal structure of the CCA-adding enzyme from Arabidopsis thaliana


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
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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

  • DOI: https://doi.org/10.1016/j.yjsbx.2025.100127
  • Primary Citation of 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.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polynucleotide adenylyltransferase family protein580Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g22660T22J18.17T22J18_17
UniProt
Find proteins for A0A1P8AU61 (Arabidopsis thaliana)
Explore A0A1P8AU61 
Go to UniProtKB:  A0A1P8AU61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8AU61
Sequence Annotations
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  • Reference Sequence
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 = 61.68α = 90
b = 63.906β = 90
c = 152.523γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

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