Molecular Cell, Volume 35
Structure and Activation Mechanism of the CHK2 DNA Damage
Zhenjian Cai, Nabil H. Chehab, and Nikola P. Pavletich
Figure S1. Sequence Alignment of CHK2 Orthologs, with Secondary Structure
Elements Indicated above the Sequences
The secondary structure elements of the FHA domain, the kinase domain and the inter-
domain linker are colored in cyan, pink and blue respectively. The different activation
loop conformations are indicated in red for the P212121 crystal form, and in green for the
P1 form. Dotted lines indicate disordered residues in the structures. Filled red circles
(red) above the sequence indicate missense mutations identified in tumors, tumor cell
lines or in Li-Fraumeni patients.
Figure S2. Superposition of the Five CHK2 Dimers from the Two Crystal Forms
The activation loops are not shown for clarity. The two protomers of the P212121 crystal
form dimer are colored in red and cyan, and those of the four dimers in the P1 form are
colored orange and green, yellow and green-yellow, pink and purple, magenta and blue.
Figure S3. Simulated Annealing (SA) Omit Electron Density of the FHA-KD Linker
and of the FHA-KD and FHA-FHA Interfaces of the P212121 Crystal Form
(A) SA omit density of the FHA-KD linker of one CHK2 protomer (residues 203-212).
The Fo-Fc electron density (yellow) was calculated after residues 203 to 212 of both
CHK2 protomers were omitted from the structure and the coordinates refined by
simulated annealing refinement from 3000 °K to remove model bias. Map was calculated
with 15.0 – 3.0 Å data and is contoured at 1.7 σ. Orientation is similar to that in Figure
(B) SA omit density of the FHA-KD interface shown in Figure 2A, in a very similar
orientation. FHA (red) residues 147-159 and 181-184, and KD (blue) residues 221-226
and 235-245 were omitted from both protomers of the model, and the coordinates were
refined by simulated annealing from 3000 °K. The Fo-Fc map was calculated with 15.0 –
3.0 Å data and was averaged across the two-fold ncs using a locally optimized ncs
operator. Only the residues omitted from the model are shown.
(C) SA omit density of the FHA-FHA interface shown in Figure 2B, in a very similar
orientation. FHA residues 95-98, 185-188 and 200-204 were omitted from both
protomers of the model, and the coordinates were refined by simulated annealing from
3000 °K. The Fo-Fc map was calculated with 15.0 – 3.0 Å data and was averaged across
the two-fold ncs using a locally optimized ncs operator. Only the residues omitted from
the model are shown.
Interkinase interface involving the αB helix (residues Arg254, Lys255, Ala257 and
Ile258) of one protomer packing in a pocket of the other protomer consisting of C lobe
residues Phe310 (αD), Val312 (αD-αE loop), Ile419 (αF) and Pro425 (αF-αG loop).