6U2G

BRAF-MEK complex with AMP-PCP bound to BRAF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Negative regulation of RAF kinase activity by ATP is overcome by 14-3-3-induced dimerization.

Liau, N.P.D.Wendorff, T.J.Quinn, J.G.Steffek, M.Phung, W.Liu, P.Tang, J.Irudayanathan, F.J.Izadi, S.Shaw, A.S.Malek, S.Hymowitz, S.G.Sudhamsu, J.

(2020) Nat Struct Mol Biol 27: 134-141

  • DOI: 10.1038/s41594-019-0365-0
  • Primary Citation of Related Structures:  
    6U2H, 6U2G

  • PubMed Abstract: 
  • The RAS-RAF-MEK-ERK signaling axis is frequently activated in human cancers. Physiological concentrations of ATP prevent formation of RAF kinase-domain (RAF KD ) dimers that are critical for activity. Here we present a 2.9-Å-resolution cry ...

    The RAS-RAF-MEK-ERK signaling axis is frequently activated in human cancers. Physiological concentrations of ATP prevent formation of RAF kinase-domain (RAF KD ) dimers that are critical for activity. Here we present a 2.9-Å-resolution crystal structure of human BRAF KD in complex with MEK and the ATP analog AMP-PCP, revealing interactions between BRAF and ATP that induce an inactive, monomeric conformation of BRAF KD . We also determine how 14-3-3 relieves the negative regulatory effect of ATP through a 2.5-Å-resolution crystal structure of the BRAF KD -14-3-3 complex, in which dimeric 14-3-3 enforces a dimeric BRAF KD assembly to increase BRAF activity. Our data suggest that most oncogenic BRAF mutations alter interactions with ATP and counteract the negative effects of ATP binding by lowering the threshold for RAF dimerization and pathway activation. Our study establishes a framework for rationalizing oncogenic BRAF mutations and provides new avenues for improved RAF-inhibitor discovery.


    Organizational Affiliation

    Department of Structural Biology, Genentech Inc., South San Francisco, USA. sudhamsu.jawahar@gene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1A394Homo sapiensMutation(s): 0 
Gene Names: MAP2K1MEK1PRKMK1
EC: 2.7.12.2
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
NIH Common Fund Data Resources
PHAROS  Q02750
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafB307Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
NIH Common Fund Data Resources
PHAROS  P15056
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download CCD File 
A, B
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.42α = 90
b = 117.42β = 90
c = 130.273γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Database references