2D4Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.330 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1038/sj.embor.7400602
  • Primary Citation of Related Structures:  
    2D4Q

  • 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 neu ...

    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.


    Related Citations: 
    • Expression, purification and preliminary crystallographic characterization of a novel segment from the neurofibromatosis type 1 protein.
      Bonneau, F., D'angelo, I., Welti, S., Ylanne, J., Stier, G., Scheffzek, K.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 2364

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeurofibrominAB257Homo sapiensMutation(s): 0 
Gene Names: neurofibrominNF1
Find proteins for P21359 (Homo sapiens)
Explore P21359 
Go to UniProtKB:  P21359
NIH Common Fund Data Resources
PHAROS  P21359
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXN
Query on OXN

Download Ideal Coordinates CCD File 
A, B
OXTOXYNOL-10
C34 H62 O11
IVKNZCBNXPYYKL-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

Download Ideal Coordinates CCD File 
B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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