Crystal structure of human 14-3-3 zeta fused to the NPM1 peptide including phosphoserine-48

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

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Structural basis for the recognition by 14-3-3 proteins of a conditional binding site within the oligomerization domain of human nucleophosmin.

Kapitonova, A.A.Tugaeva, K.V.Varfolomeeva, L.A.Boyko, K.M.Cooley, R.B.Sluchanko, N.N.

(2022) Biochem Biophys Res Commun 627: 176-183

  • DOI: https://doi.org/10.1016/j.bbrc.2022.08.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nucleophosmin 1 (NPM1) is a multifunctional protein regulating ribosome biogenesis, centrosome duplication and chromatin remodeling. Being a major nucleolar protein, NPM1 can migrate to the nucleus and the cytoplasm, which is controlled by changes of NPM1 oligomerization and interaction with other cell factors. NPM1 forms a stable pentamer with its N-terminal structured domain, where two nuclear export signals and several phosphorylation sites reside. This domain undergoes dissociation and disordering upon Ser48 phosphorylation in the subunit interface. Recent studies indicated that Ser48 is important for NPM1 interaction with other proteins including 14-3-3, the well-known phosphoserine/phosphothreonine binders, but the structural basis for 14-3-3/NPM1 interaction remained unaddressed. By fusing human 14-3-3ζ with an NPM1 segment surrounding Ser48, which was phosphorylated inside Escherichia coli cells by co-expressed protein kinase A, here we obtained the desired protein/phosphopeptide complex and determined its crystal structure. While biochemical data indicated that the interaction is driven by Ser48 phosphorylation, the crystallographic 14-3-3/phosphopeptide interface reveals an NPM1 conformation distinctly different from that in the NPM1 pentamer. Given the canonical phosphopeptide-binding mode observed in our crystal structure, Ser48 emerges as a conditional binding site whose recognition by 14-3-3 proteins is enabled by NPM1 phosphorylation, disassembly and disordering under physiological circumstances.

  • Organizational Affiliation

    A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein zeta/delta,NucleophosminA,
B [auth C]
248Homo sapiensMutation(s): 7 
UniProt & NIH Common Fund Data Resources
Find proteins for P06748 (Homo sapiens)
Explore P06748 
Go to UniProtKB:  P06748
PHAROS:  P06748
GTEx:  ENSG00000181163 
Find proteins for P63104 (Homo sapiens)
Explore P63104 
Go to UniProtKB:  P63104
PHAROS:  P63104
GTEx:  ENSG00000164924 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP06748P63104
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SEP
B [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.696α = 90
b = 110.207β = 90
c = 163.413γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-15-2021-1354
Russian Science FoundationRussian Federation19-74-10031

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description