3V42 | pdb_00003v42

Crystal structure of renal tumor suppressor protein, folliculin

• PDB DOI: https://doi.org/10.2210/pdb3V42/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-14 Released: 2012-08-15 
• Deposition Author(s): Nookala, R.K., Chirgadze, D.Y., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer.

Nookala, R.K., Langemeyer, L., Pacitto, A., Ochoa-Montano, B., Donaldson, J.C., Blaszczyk, B.K., Chirgadze, D.Y., Barr, F.A., Bazan, J.F., Blundell, T.L.

(2012) Open Biol 2: 120071-120071

• PubMed: 22977732 
• DOI: https://doi.org/10.1098/rsob.120071
• Primary Citation Related Structures: 
  3V42


• PubMed Abstract: 
  

  Mutations in the renal tumour suppressor protein, folliculin, lead to proliferative skin lesions, lung complications and renal cell carcinoma. Folliculin has been reported to interact with AMP-activated kinase, a key component of the mammalian target of rapamycin pathway. Most cancer-causing mutations lead to a carboxy-terminal truncation of folliculin, pointing to a functional importance of this domain in tumour suppression. We present here the crystal structure of folliculin carboxy-terminal domain and demonstrate that it is distantly related to differentially expressed in normal cells and neoplasia (DENN) domain proteins, a family of Rab guanine nucleotide exchange factors (GEFs). Using biochemical analysis, we show that folliculin has GEF activity, indicating that folliculin is probably a distantly related member of this class of Rab GEFs.

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Organizational Affiliation: 
• Department of Biochemistry , University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.93 kDa 
• Atom Count: 3,308 
• Modeled Residue Count: 395 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Folliculin	A, B	226	Homo sapiens	Mutation(s): 3  Gene Names: BHD, FLCN
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFG4 (Homo sapiens) Explore Q8NFG4  Go to UniProtKB:  Q8NFG4
PHAROS:  Q8NFG4 GTEx:  ENSG00000154803

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.05	α = 90
b = 99.951	β = 90
c = 107.584	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Nookala, R.K., Chirgadze, D.Y., Blundell, T.L.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description