8ZAJ | pdb_00008zaj

Cryo-EM structure of a 55 kDa nucleoplasmin domain of AtFKBP53


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

2.0 angstrom cryo-EM structure of the 55 kDa nucleoplasmin domain of AtFKBP53.

Bharambe, N.Saharan, K.Vasudevan, D.Basak, S.

(2025) J Struct Biol 217: 108203-108203

  • DOI: https://doi.org/10.1016/j.jsb.2025.108203
  • Primary Citation of Related Structures:  
    8ZAJ

  • PubMed Abstract: 

    The knowledge of three-dimensional structures of biological macromolecules is crucial for understanding the molecular mechanisms underlying disease pathology and for devising drugs targeting specific molecules. Single particle cryo-electron microscopy (Cryo-EM) has become indispensable for this purpose, particularly for large macromolecules and their complexes. However, its effectiveness has been limited in achieving near-atomic resolution for smaller macromolecules. This study presents the Cryo-EM structure of a 55 kDa pentameric AtFKBP53 nucleoplasmin domain at 2.0 Å nominal resolution. Our approach involves selecting the optimal grid for data collection and precise alignment of small particles to enhance the resolution of the final 3D reconstructed map. In this study, we systematically processed cryo-EM dataset of a small molecule to improve alignment, and this data processing strategy can be used as a guidance to process the cryo-EM data of other small molecules.


  • Organizational Affiliation
    • School of Biological Sciences, Nanyang Technological University, 637551, Singapore.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP53
A, B, C, D, E
108Arabidopsis thalianaMutation(s): 0 
Gene Names: FKBP53At4g25340T30C3_20
EC: 5.2.1.8
UniProt
Find proteins for Q93ZG9 (Arabidopsis thaliana)
Explore Q93ZG9 
Go to UniProtKB:  Q93ZG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93ZG9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSingaporeNRF

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release