6PP9

Crystal structure of BRAF:MEK1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes.

Park, E.Rawson, S.Li, K.Kim, B.W.Ficarro, S.B.Pino, G.G.Sharif, H.Marto, J.A.Jeon, H.Eck, M.J.

(2019) Nature 575: 545-550

  • DOI: 10.1038/s41586-019-1660-y

  • PubMed Abstract: 
  • RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival <sup>1-3 </sup>. RAF activity is tightly regulated, and inappropriate activation is a ...

    RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival 1-3 . RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer 4-6 . At present, the structural basis of RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo-electron microscopy (cryo-EM). A 4.1 Å resolution cryo-EM reconstruction reveals an inactive BRAF-MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. hjeon@crystal.harvard.edu.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. eck@crystal.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. hjeon@crystal.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. eck@crystal.harvard.edu.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A
283Homo sapiensMutation(s): 0 
Gene Names: BRAF (BRAF1, RAFB1)
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to Gene View: BRAF
Go to UniProtKB:  P15056
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dual specificity mitogen-activated protein kinase kinase 1
B
397Homo sapiensMutation(s): 2 
Gene Names: MAP2K1 (MEK1, PRKMK1)
EC: 2.7.12.2
Find proteins for Q02750 (Homo sapiens)
Go to Gene View: MAP2K1
Go to UniProtKB:  Q02750
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

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A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LCJ
Query on LCJ

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B
5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide
C16 H14 F I N4 O3
RFWVETIZUQEJEF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.697α = 90.00
b = 116.697β = 90.00
c = 130.944γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP50 CA165962
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR50 CA221830

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references
  • Version 1.2: 2019-12-04
    Type: Author supporting evidence, Database references