Primary Citation PubMed: 23273428
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Published in 2014
46 The DFG-out inactive conformation was obtained from PDB entry 4I20.
Three crystal structures, 2ITW, 3W32, and 4I20 are the DFG-in active form (A), Src-like inactive form (T), and DFG-out inactive form (I), respectively.
Table 1 Comparison of Three EGFR Crystal Structures a RMSD (Å) crystal structure backbone A-loop DFG distance of ion pair (Å) 2ITW (A) 0 0 0 8.7 3W32 (T) 4.4 10.5 3.7 14.4 4I20 (I) 3.3 2.9 6.7 12.4 a The crystal structure of 2ITW (A) is used as the reference structure for RMSD calculations.
The RMSD values are calculated with respect to the target structure (2ITW, 3W32, or 4I20).
ref structure backbone A-loop DFG av distance of ion pair (Å) ATI pathway 0 3W32 (T) 2.1 2.7 1.6 15.5 2 4I20 (I) 2.6 2.1 1.5 15.0 7 2ITW (A) 5.4 11.2 6.6 12.9 11 2ITW (A) 2.4 2.8 1.9 8.5 14 2ITW (A) 4.4 4.0 3.9 13.6 31 2ITW (A) 4.2 5.6 6.0 13.9 AI pathway 0 4I20 (I) 2.6 2.2 1.5 16.0 1 2ITW (A) 3.4 3.2 4.4 15.9 3 2ITW (A) 2.3 3.3 1.8 8.4 7 2ITW (A) 3.9 3.9 6.9 11.9 9 2ITW (A) 4.0 4.1 6.2 9.7 Further examination of fluctuation of the structural properties shows that EGFR undergoes conformational transitions in some classes, though it is pretty stable in most of the classes (for the top 20 populated classes, see SI Figure S4).
Publication Year: 2014
Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.
(2014) PLoS One 9
PubMed: 25427151 | PubMedCentral: PMC4245119 | DOI: 10.1371/journal.pone.0113488
The inactive EGFR crystal structures included the following pdb entries: pdb id 2GS7 (Cdk/Src-IF1 EGFR-WT in complex with AMP-PNP); pdb id 1XKK (Cdk/Src-IF1, EGFR-WT in complex with Lapatinib); pdb id... 2RFE (Cdk/Src-IF1, EGFR-WT in complex with a 40-residue MIG peptide); pdb id 2RF9 (Cdk/Src-IF2, EGFR-WT in complex with a 60-residue MIG6 peptide); pdb id 4I20 (Cdk/Src-IF2, Apo EGFR-L858R, V948R); pdb id 4I1Z (Cdk/Src-IF2, Apo EGFR-L858R/T790M, V948R); and pdb id 4I21(Cdk/Src-IF2,EGFR-L858R/T790M in complex with MIG6).
Structural similarities in the functional regions of the Cdk/Src-IF2 EGFR-WT conformation (in blue), DFG-out/αC-helix-out (pdb id 2RF9); Cdk/Src-IF2 EGFR-L858R conformation (in red), DFG-out/αC-helix-out (pdb id 4I20); and Cdk/Src-IF2 EGFR-L858R/T790M double mutant conformation (in green), DFG-out/αC-helix-out (pdb id 4I21).
The computed B-factors describe time-averaged fluctuations of heavy atoms obtained from simulations of (A) Cdk/Src-IF1 EGFR-WT (pdb id 1XKK, in blue), (B) Cdk/Src-IF2 EGFR-WT (pdb id 2RF9, in red), (C) active EGFR-WT (pdb id 2ITX, in green), (D) active EGFR-L858R (pdb id 2ITV, in red), (E) active EGFR-T790M (pdb id 2JIT, in green), (F) inactive EGFR-L858R (pdb id 4I20, in red), (G) inactive EGFR-L858R/T790M (pdb id 4I21, in green), (H) inactive ErbB4-WT (pdb id 3BBT, in green), (I) active ErbB4-WT (pdb id 3BCE, in maroon).
C) The computed B-factors for Cdk/Src-IF2 structures of EGFR-WT (pdb id 2RF9, in blue), EGFR-L858R (pdb id 4I20, in red), and EGFR-L858R/T790M (pdb id 4I21, in green).
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