2D4Q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 

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
  • Also Cited By: 2E2X

  • 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.,SECT.D 60: 2364

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neurofibromin
A, B
257Homo sapiensMutation(s): 0 
Gene Names: NF1
Find proteins for P21359 (Homo sapiens)
Go to Gene View: NF1
Go to UniProtKB:  P21359
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP
Download SDF File 
Download CCD File 
B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
OXN
Query on OXN
Download SDF File 
Download CCD File 
A, B
OXTOXYNOL-10
ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL); TRITON X-100
C34 H62 O11
IVKNZCBNXPYYKL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.500α = 90.00
b = 113.500β = 90.00
c = 125.600γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
CNSrefinement
MOSFLMdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance