8AS5

CryoEM structure of the human Nucleophosmin 1 core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1.

Saluri, M.Leppert, A.Gese, G.V.Sahin, C.Lama, D.Kaldmae, M.Chen, G.Elofsson, A.Allison, T.M.Arsenian-Henriksson, M.Johansson, J.Lane, D.P.Hallberg, B.M.Landreh, M.

(2023) PNAS Nexus 2: pgac303-pgac303

  • DOI: https://doi.org/10.1093/pnasnexus/pgac303
  • Primary Citation of Related Structures:  
    8AS5

  • PubMed Abstract: 

    How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant nucleolar protein that forms large oligomers and undergoes liquid-liquid phase separation by binding RNA or ribosomal proteins. It provides the scaffold for ribosome assembly but also prevents protein aggregation as part of the cellular stress response. Here, we use aggregation assays and native mass spectrometry (MS) to examine the relationship between the self-assembly and chaperone activity of NPM1. We find that oligomerization of full-length NPM1 modulates its ability to retard amyloid formation in vitro. Machine learning-based structure prediction and cryo-electron microscopy reveal fuzzy interactions between the acidic disordered region and the C-terminal nucleotide-binding domain, which cross-link NPM1 pentamers into partially disordered oligomers. The addition of basic peptides results in a tighter association within the oligomers, reducing their capacity to prevent amyloid formation. Together, our findings show that NPM1 uses a "grappling hook" mechanism to form a network-like structure that traps aggregation-prone proteins. Nucleolar proteins and RNAs simultaneously modulate the association strength and chaperone activity, suggesting a mechanism by which nucleolar composition regulates the chaperone activity of NPM1.


  • Organizational Affiliation

    Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleophosmin
A, B, C, D, E
295Homo sapiensMutation(s): 0 
Gene Names: NPM1NPM
UniProt & NIH Common Fund Data Resources
Find proteins for P06748 (Homo sapiens)
Explore P06748 
Go to UniProtKB:  P06748
PHAROS:  P06748
GTEx:  ENSG00000181163 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06748
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0352

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden2017.0080

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release