AtFKBP53 N-terminal Nucleoplasmin Domain

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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This is version 1.3 of the entry. See complete history


AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains.

Singh, A.K.Datta, A.Jobichen, C.Luan, S.Vasudevan, D.

(2020) Nucleic Acids Res 48: 1531-1550

  • DOI: https://doi.org/10.1093/nar/gkz1153
  • Primary Citation of Related Structures:  
    6J2M, 6J2Z

  • PubMed Abstract: 

    FKBP53 is one of the seven multi-domain FK506-binding proteins present in Arabidopsis thaliana, and it is known to get targeted to the nucleus. It has a conserved PPIase domain at the C-terminus and a highly charged N-terminal stretch, which has been reported to bind to histone H3 and perform the function of a histone chaperone. To better understand the molecular details of this PPIase with histone chaperoning activity, we have solved the crystal structures of its terminal domains and functionally characterized them. The C-terminal domain showed strong PPIase activity, no role in histone chaperoning and revealed a monomeric five-beta palm-like fold that wrapped over a helix, typical of an FK506-binding domain. The N-terminal domain had a pentameric nucleoplasmin-fold; making this the first report of a plant nucleoplasmin structure. Further characterization revealed the N-terminal nucleoplasmin domain to interact with H2A/H2B and H3/H4 histone oligomers, individually, as well as simultaneously, suggesting two different binding sites for H2A/H2B and H3/H4. The pentameric domain assists nucleosome assembly and forms a discrete complex with pre-formed nucleosomes; wherein two pentamers bind to a nucleosome.

  • Organizational Affiliation

    Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP53108Arabidopsis thalianaMutation(s): 0 
Gene Names: FKBP53At4g25340T30C3_20
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.59α = 90
b = 97.39β = 94.12
c = 96.43γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description