6J2M

Crystal structure of AtFKBP53 C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 
    0.145 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.125 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FK5Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP53123Arabidopsis 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download Ideal Coordinates CCD File 
B [auth A]8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free:  0.145 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.125 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 0.126 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.04α = 90
b = 48.19β = 90
c = 59.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FK5Click on this verticalbar to view details

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