1K5J

The Crystal Structure of Nucleoplasmin-Core

• PDB DOI: https://doi.org/10.2210/pdb1K5J/pdb

• Classification: CHAPERONE
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-10-10 Released: 2001-11-01 
• Deposition Author(s): Dutta, S., Akey, I.V., Dingwall, C., Hartman, K.L., Laue, T., Nolte, R.T., Head, J.F., Akey, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.251 

Literature

The crystal structure of nucleoplasmin-core: implications for histone binding and nucleosome assembly.

Dutta, S., Akey, I.V., Dingwall, C., Hartman, K.L., Laue, T., Nolte, R.T., Head, J.F., Akey, C.W.

(2001) Mol Cell 8: 841-853

• PubMed: 11684019 
• DOI: https://doi.org/10.1016/s1097-2765(01)00354-9
• Primary Citation of Related Structures:  
  1K5J


• PubMed Abstract: 
  

  The efficient assembly of histone complexes and nucleosomes requires the participation of molecular chaperones. Currently, there is a paucity of data on their mechanism of action. We now present the structure of an N-terminal domain of nucleoplasmin (Np-core) at 2.3 A resolution. The Np-core monomer is an eight-stranded beta barrel that fits snugly within a stable pentamer. In the crystal, two pentamers associate to form a decamer. We show that both Np and Np-core are competent to assemble large complexes that contain the four core histones. Further experiments and modeling suggest that these complexes each contain five histone octamers which dock to a central Np decamer. This work has important ramifications for models of histone storage, sperm chromatin decondensation, and nucleosome assembly.

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Organizational Affiliation: 

Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.76 kDa 
• Atom Count: 3,627 
• Modelled Residue Count: 462 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoplasmin Core	A, B, C, D, E	124	Xenopus laevis	Mutation(s): 2  Gene Names: Nucleoplasmin
UniProt
Find proteins for P05221 (Xenopus laevis) Explore P05221  Go to UniProtKB:  P05221

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.251 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.7	α = 90
b = 67.1	β = 123.3
c = 101.7	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-01 
Deposition Author(s): Dutta, S., Akey, I.V., Dingwall, C., Hartman, K.L., Laue, T., Nolte, R.T., Head, J.F., Akey, C.W.

Revision History  

• Version 1.0: 2001-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection