4N8M | pdb_00004n8m

Structural polymorphism in the N-terminal oligomerization domain of NPM1

• PDB DOI: https://doi.org/10.2210/pdb4N8M/pdb

• Classification: CHAPERONE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-17 Released: 2014-03-12 
• Deposition Author(s): Mitrea, D., Royappa, G., Buljan, M., Yun, M., Pytel, N., Satumba, J., Nourse, A., Park, C., Babu, M.M., White, S.W., Kriwacki, R.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.190 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Structural polymorphism in the N-terminal oligomerization domain of NPM1.

Mitrea, D.M., Grace, C.R., Buljan, M., Yun, M.K., Pytel, N.J., Satumba, J., Nourse, A., Park, C.G., Madan Babu, M., White, S.W., Kriwacki, R.W.

(2014) Proc Natl Acad Sci U S A 111: 4466-4471

• PubMed: 24616519 
• DOI: https://doi.org/10.1073/pnas.1321007111
• Primary Citation Related Structures: 
  4N8M


• PubMed Abstract: 
  

  Nucleophosmin (NPM1) is a multifunctional phospho-protein with critical roles in ribosome biogenesis, tumor suppression, and nucleolar stress response. Here we show that the N-terminal oligomerization domain of NPM1 (Npm-N) exhibits structural polymorphism by populating conformational states ranging from a highly ordered, folded pentamer to a highly disordered monomer. The monomer-pentamer equilibrium is modulated by posttranslational modification and protein binding. Phosphorylation drives the equilibrium in favor of monomeric forms, and this effect can be reversed by Npm-N binding to its interaction partners. We have identified a short, arginine-rich linear motif in NPM1 binding partners that mediates Npm-N oligomerization. We propose that the diverse functional repertoire associated with NPM1 is controlled through a regulated unfolding mechanism signaled through posttranslational modifications and intermolecular interactions.

---

Organizational Affiliation: 
• Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105.

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: 73.37 kDa 
• Atom Count: 4,263 
• Modeled Residue Count: 532 
• Deposited Residue Count: 665 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleophosmin	A, B, C, D, E	133	Mus musculus	Mutation(s): 0  Gene Names: Npm1
UniProt
Find proteins for Q61937 (Mus musculus) Explore Q61937  Go to UniProtKB:  Q61937

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.190 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.675	α = 90
b = 69.794	β = 99.87
c = 88.63	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Mitrea, D., Royappa, G., Buljan, M., Yun, M., Pytel, N., Satumba, J., Nourse, A., Park, C., Babu, M.M., White, S.W., Kriwacki, R.W.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2019-11-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description