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 8EDM | pdb_00008edm

Cryo-EM structure of the full-length human NF1 dimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8EDM

This is version 1.2 of the entry. See complete history. 

Literature

Destabilizing NF1 variants act in a dominant negative manner through neurofibromin dimerization.

Young, L.C., Goldstein de Salazar, R., Han, S.W., Huang, Z.Y.S., Merk, A., Drew, M., Darling, J., Wall, V., Grisshammer, R., Cheng, A., Allison, M.R., Sale, M.J., Nissley, D.V., Esposito, D., Ognjenovic, J., McCormick, F.

(2023) Proc Natl Acad Sci U S A 120: e2208960120-e2208960120

  • DOI: https://doi.org/10.1073/pnas.2208960120
  • Primary Citation Related Structures: 
    8E20, 8EDM

  • PubMed Abstract: 

    The majority of pathogenic mutations in the neurofibromatosis type I ( NF1 ) gene reduce total neurofibromin protein expression through premature truncation or microdeletion, but it is less well understood how loss-of-function missense variants drive NF1 disease. We have found that patient variants in codons 844 to 848, which correlate with a severe phenotype, cause protein instability and exert an additional dominant-negative action whereby wild-type neurofibromin also becomes destabilized through protein dimerization. We have used our neurofibromin cryogenic electron microscopy structure to predict and validate other patient variants that act through a similar mechanism. This provides a foundation for understanding genotype-phenotype correlations and has important implications for patient counseling, disease management, and therapeutics.


  • Organizational Affiliation: 
    • Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94153.

Macromolecule Content 

  • Total Structure Weight: 634.82 kDa 
  • Atom Count: 2,509 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 5,636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform I of Neurofibromin
A, B
2,818Homo sapiensMutation(s): 0 
Gene Names: NF1
UniProt & NIH Common Fund Data Resources
Find proteins for P21359 (Homo sapiens)
Explore P21359 
Go to UniProtKB:  P21359
PHAROS:  P21359
GTEx:  ENSG00000196712 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21359
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references
  • Version 1.2: 2025-05-21
    Changes: Data collection, Structure summary