Crystal structure of the Sec-PH domain of the human neurofibromatosis type 1 protein

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.330 

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A novel bipartite phospholipid-binding module in the neurofibromatosis type 1 protein

D'angelo, I.Welti, S.Bonneau, F.Scheffzek, K.

(2006) EMBO Rep 7: 174-179

  • DOI: https://doi.org/10.1038/sj.embor.7400602
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Neurofibromatosis type 1 (NF1) is a common tumour predisposition syndrome associated with numerous clinical complications. Mutations in the tumour suppressor gene NF1 are responsible for disease pathogenesis. This gene encodes the 320 kDa protein neurofibromin, the only clearly defined function of which is to act as a Ras-specific GTPase-activating protein (RasGAP). Here we report the structural discovery of a novel module in neurofibromin, composed of a Sec14p homologous segment and a previously undetected pleckstrin homology (PH)-like domain of potentially novel function. We show phospholipid binding by this bipartite module and identify residues that are involved in this activity; we also show that the PH-like domain is not sufficient for lipid binding. The unique architecture of the domain interface points to a model of how the PH-like domain may regulate binding of a ligand by the Sec14 module.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
257Homo sapiensMutation(s): 0 
Gene Names: neurofibromin
Membrane Entity: Yes 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.330 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.5α = 90
b = 113.5β = 90
c = 125.6γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations