4WO5 | pdb_00004wo5

Crystal structure of a BRAF kinase domain monomer

• PDB DOI: https://doi.org/10.2210/pdb4WO5/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2014-10-15 Released: 2014-12-03 
• Deposition Author(s): Critton, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.260 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation.

Thevakumaran, N., Lavoie, H., Critton, D.A., Tebben, A., Marinier, A., Sicheri, F., Therrien, M.

(2015) Nat Struct Mol Biol 22: 37-43

• PubMed: 25437913 
• DOI: https://doi.org/10.1038/nsmb.2924
• Primary Citation Related Structures: 
  4WO5


• PubMed Abstract: 
  

  Reported RAF kinase domain structures adopt a side-to-side dimer configuration reflective of an 'on' state that underpins an allosteric mechanism of regulation. Atomic details of the monomer 'off' state have been elusive. Reinspection of the BRAF kinase domain structures revealed that sulfonamide inhibitors induce features of an off state, primarily a laterally displaced helix αC stabilized by the activation segment helix 1 (AS-H1). These features correlated with the ability of sulfonamides to disrupt human BRAF homodimers in cells, in vitro and in crystals yielding a structure of BRAF in a monomer state. The crystal structure revealed exaggerated, nonproductive positions of helix αC and AS-H1, the latter of which is the target of potent BRAF oncogenic mutations. Together, this work provides formal proof of an allosteric link between the RAF dimer interface, the activation segment and the catalytic infrastructure.

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Organizational Affiliation: 
• 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. [2] Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada.
Molecular Structure &Design Group, Molecular Discovery Technologies Department, Bristol-Myers Squibb Research, Princeton, New Jersey, USA.
1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. [2] Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
1] Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada. [2] Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Québec, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.06 kDa 
• Atom Count: 4,109 
• Modeled Residue Count: 523 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	300	Homo sapiens	Mutation(s): 16  Gene Names: BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens) Explore P15056  Go to UniProtKB:  P15056
PHAROS:  P15056 GTEx:  ENSG00000157764

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
324	C [auth A], D [auth B]	N-{3-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-difluorophenyl}propane-1-sulfonamide C17 H14 Cl F2 N3 O3 S YZDJQTHVDDOVHR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.260 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.61	α = 90
b = 72.748	β = 90
c = 243.338	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Critton, D.A.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2015-01-14
  Changes: Database references
• Version 1.3: 2015-02-04
  Changes: Derived calculations
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy