For each protein of the Raf Protein family, which Braf is apart of, there are three conserved domains: CR1, CR2, and CR3, in order from the N terminus to the C terminus of the protein. CR1 contains the Ras binding domain and zinc ion binding locations. CR2 has many serine and threonine residues that are used for regulation of the protein's functioning. CR3 is the kinase domain. (27)

Raf kinase domains have a small N lobe and larger C lobe, which can move relative to each other and control ATP binding and conformation. In the large lobe, there is a conserved DFG amino acid sequence for protein activation. In Braf, there is a conserved KDD motif for ATP binding (K576). (27)

The two lobes can move from an open conformation (for ATP binding or ADP release) to a closed conformation (for bringing protein residues into the catalytic site of the protein). (27)

An entire 3D structure of the 766 amino acid structure of Braf is unavailable. No 3D structures of other Raf proteins are available either. The structure of Braf would most likely resemble other proteins with serine/threonine kinase domains and functions, which is discussed below. (26)

1) Catalytic Domain of Braf, Raf Kinases (Residues 463-715)

This conserved domain of Braf is responsible for the transfer of a phosphoryl group from ATP to either a serine or threonine residue on a different protein. These domains are specific to serine/threonine kinases of the Raf family of proteins. (7)

2) Protein Kinase Domain (Residues 458-713)

This is a multi-domain spanning conserved domain of the Braf protein. Kinase domains are responsible for the phosphorylation of certain residues of protein substrates. (7)

3) Ubituitin domain of Raf serine/threonine kinases aka Ras Binding Domain (Residues 156-227)

The Ras binding domain of Braf is structurally conserved to ubiquitin (Ubq). This is despite no sequence similarity between the proteins, but suggests that Braf is apart of the Ubq superfamily). (7)

4) Phorbol esters/diacylglycerol binding domain (C1) (Residues 235-280)

This Phorbol esters/diacylglycerol binding domain is also referred to as the Protein kinase C conserved region domain (C1), and is a conserved sequence across members of the C1 superfamily. This domain is responsible for organizing phorbol ester of diacylglycerol signaling molecules in RasGRPs. (7)

No 3D model of this domain has been determined yet for the Braf protein.

As seen in the diagram above describing the secondary structures of Braf, we can see that Braf contains both the alpha-helices secondary structure and beta-sheets. Additionally, there are numerous turns in the direction of the protein contributing to the overall secondary structures. (26)

Braf's catalytic domain of the serine/threonine protein, Ras (residues 463-715) and its overlapping Kinase domain (residues 458-713) are made of alpha-helices, beta-sheets, and turns. (26)

The ubiquitin domain (residues 156-227) also contains all 3 secondary structures discussed within its smaller span of the protein. (26)

There are no alpha-helices, beta-sheets, or turns reported within the phorbol esters/diacylglycerol binding domain of Braf (residues 235-280). (26)

In its dimerized form, Braf is more efficient at phosphorylating its substrates compared to when it is in its monomer form. (13)

The heterodimer formed between Raf-1 and Braf further increases phosphorylation efficiency compared to the Braf/Braf homodimer. Raf must dimerize in order to function and continue the Raf signaling pathway, however, Braf mutants can still function without dimerization. (13)