Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.57 kDa 
• Atom Count: 4320 
• Modelled Residue Count: 512 
• Deposited Residue Count: 514 
• Unique protein chains: 1

2D4Q

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

• PDB DOI: 10.2210/pdb2D4Q/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-10-22 Released: 2006-03-07 
• Deposition Author(s): D'angelo, I., Welti, S., Bonneau, F., Scheffzek, K.

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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 

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

• PubMed: 16397625 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurofibromin	A, B	257	Homo sapiens	Mutation(s): 0  Gene Names: neurofibromin, NF1
UniProt & NIH Common Fund Data Resources
Find proteins for P21359 (Homo sapiens) Explore P21359  Go to UniProtKB:  P21359
PHAROS:  P21359

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXN	C [auth A], D [auth B]	OXTOXYNOL-10 C34 H62 O11 IVKNZCBNXPYYKL-UHFFFAOYSA-N
POP	E [auth B], F [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

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 = 113.5	α = 90
b = 113.5	β = 90
c = 125.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-22 
• Released Date: 2006-03-07 
Deposition Author(s): D'angelo, I., Welti, S., Bonneau, F., Scheffzek, K.

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