1UWH

The complex of wild type B-RAF and BAY439006.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of Activation of the Raf-Erk Signaling Pathway by Oncogenic Mutations of B-Raf

Wan, P.T.C.Garnett, M.J.Roe, S.M.Lee, S.Niculescu-Duvaz, D.Good, V.M.Jones, C.M.Marshall, C.J.Springer, C.J.Barford, D.Marais, R.

(2004) Cell 116: 855

  • DOI: 10.1016/s0092-8674(04)00215-6
  • Primary Citation of Related Structures:  
    1UWJ, 1UWH

  • PubMed Abstract: 
  • Over 30 mutations of the B-RAF gene associated with human cancers have been identified, the majority of which are located within the kinase domain. Here we show that of 22 B-RAF mutants analyzed, 18 have elevated kinase activity and signal to ERK in ...

    Over 30 mutations of the B-RAF gene associated with human cancers have been identified, the majority of which are located within the kinase domain. Here we show that of 22 B-RAF mutants analyzed, 18 have elevated kinase activity and signal to ERK in vivo. Surprisingly, three mutants have reduced kinase activity towards MEK in vitro but, by activating C-RAF in vivo, signal to ERK in cells. The structures of wild type and oncogenic V599EB-RAF kinase domains in complex with the RAF inhibitor BAY43-9006 show that the activation segment is held in an inactive conformation by association with the P loop. The clustering of most mutations to these two regions suggests that disruption of this interaction converts B-RAF into its active conformation. The high activity mutants signal to ERK by directly phosphorylating MEK, whereas the impaired activity mutants stimulate MEK by activating endogenous C-RAF, possibly via an allosteric or transphosphorylation mechanism.


    Organizational Affiliation

    Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASEAB276Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BAX
Query on BAX

Download CCD File 
A, B
4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE
C21 H16 Cl F3 N4 O3
MLDQJTXFUGDVEO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BAXIC50:  120   nM  BindingDB
BAXIC50:  114   nM  BindingDB
BAXKd:  260   nM  BindingDB
BAXKd:  284   nM  BindingDB
BAXIC50:  15   nM  BindingDB
BAXIC50:  200   nM  BindingDB
BAXIC50:  12   nM  BindingDB
BAXIC50:  11   nM  BindingDB
BAXIC50 :  22   nM  PDBBind
BAXIC50:  130   nM  BindingDB
BAXIC50:  136   nM  BindingDB
BAXIC50:  76.19999694824219   nM  BindingDB
BAXIC50:  7300   nM  BindingDB
BAXIC50:  26   nM  BindingDB
BAXIC50:  6599   nM  BindingDB
BAXKd:  54   nM  BindingDB
BAXIC50:  24   nM  BindingDB
BAXIC50:  6100   nM  BindingDB
BAXIC50:  23   nM  BindingDB
BAXIC50:  22   nM  BindingDB
BAXIC50:  310   nM  BindingDB
BAXIC50:  4.400000095367432   nM  BindingDB
BAXIC50:  12.699999809265137   nM  BindingDB
BAXKi:  22   nM  BindingDB
BAXEC50:  3   nM  BindingDB
BAXIC50:  52   nM  BindingDB
BAXIC50:  46   nM  BindingDB
BAXIC50:  43   nM  BindingDB
BAXIC50:  42   nM  BindingDB
BAXIC50:  38   nM  BindingDB
BAXKi:  38   nM  BindingDB
BAXKd:  540   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.28α = 90
b = 110.28β = 90
c = 143.01γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
BEASTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-19
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Structure summary