Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 635.36 kDa 
• Atom Count: 36,250 
• Modelled Residue Count: 4,555 
• Deposited Residue Count: 5,636 
• Unique protein chains: 1

 7R04

Neurofibromin in open conformation

• PDB DOI: 10.2210/pdb7R04/pdb
• EM Map EMD-14219: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-02-01 Released: 2022-03-30 
• Deposition Author(s): Chaker-Margot, M., Scheffzek, K., Maier, T.
• Funding Organization(s): Human Frontier Science Program (HFSP)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of activation of the tumor suppressor protein neurofibromin.

Chaker-Margot, M., Werten, S., Dunzendorfer-Matt, T., Lechner, S., Ruepp, A., Scheffzek, K., Maier, T.

(2022) Mol Cell 82: 1288

• PubMed: 35353986 
• DOI: 10.1016/j.molcel.2022.03.011
• Primary Citation of Related Structures:  
  7R03, 7R04


• PubMed Abstract: 
  

Mutations in the NF1 gene cause the familial genetic disease neurofibromatosis type I, as well as predisposition to cancer. The NF1 gene product, neurofibromin, is a GTPase-activating protein and acts as a tumor suppressor by negatively regulating the small GTPase, Ras. However, structural insights into neurofibromin activation remain incompletely defined. Here, we provide cryoelectron microscopy (cryo-EM) structures that reveal an extended neurofibromin homodimer in two functional states: an auto-inhibited state with occluded Ras-binding site and an asymmetric open state with an exposed Ras-binding site. Mechanistically, the transition to the active conformation is stimulated by nucleotide binding, which releases a lock that tethers the catalytic domain to an extended helical repeat scaffold in the occluded state. Structure-guided mutational analysis supports functional relevance of allosteric control. Disease-causing mutations are mapped and primarily impact neurofibromin stability. Our findings suggest a role for nucleotides in neurofibromin regulation and may lead to therapeutic modulation of Ras signaling.

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Organizational Affiliation: 

Biozentrum, University of Basel, 4056 Basel, Switzerland. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform I of Neurofibromin	A, B	2,818	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSP (Subject of Investigation/LOI)	C [auth A]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.14
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Chaker-Margot, M., Scheffzek, K., Maier, T.

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Funding Organization	Location	Grant Number
Human Frontier Science Program (HFSP)	Switzerland	--

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references
• Version 1.2: 2022-04-20
  Changes: Database references