iCn3D Skill: Aligning two structures
- Page ID
- 114628
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Superimpose and annotate active (phosphorylated) form of cyclin-dependent kinase 2 (1JST) and inactive (1FIN)
Description
1JST (active)
- PHOSPHORYLATED CYCLIN-DEPENDENT KINASE-2 BOUND TO CYCLIN A. Has bound Mn2+ and ATPγS.
- pT160 is on the regulatory T-loop of CDK2. It is mostly buried and neutralized by 3 Arg side chains. Compared to unphosphorylated CDK2–CyclinA, the T-loop moves by as much as 7 Å,
- T loop about 147-163
1FIN (inactive):
- CYCLIN A-CYCLIN-DEPENDENT KINASE 2 COMPLEX. Has a bound ATP as well as Cyclin A (B and D chains)
Instructions
- File, Align, Structure to Structure
- Input 1JST and 1FIN
- Choose All Matching Molecules Superimposed
- In the Select residues in aligned alignment window, click the blue font 1JST-C to select the entire chain. Color, Green, Dark Green (green for go = active)
- Likewise, select 1FIN-A. Color, Yellow, Yellow (so we can color the T loop red)
- Alt Click in the modeling window MN and ctrl Click ATP. Select, Save Selection, MN_ATP
- Style, Chemicals, Sphere
- In long sequences, capture with mouse approx T loop 147-163. Select, Save Selection, T loops; Color red
- In the long sequences, hover over and then click to select in 1JST_C x160 (this is phospho-Thr160) and then in 1FIN_A T160 (i.e. Thr 160). Select, Save Selection, Thr160s
- Style, Sidechains, Sticks
- Color, Atom
- In the Defined Sets, click then ctrl click all of the selections you made: MnATP, Thr160s, align_1FIN_A, and align_1JST_C. Then save as 000All. Using 000 at the start of the name put the combined selection at the top of the Defined Sets window. This will be important later.
- Make sure 000All is selected, then View, View Selection
- Style, Background, White
- File, Share Link, Lifelong Short Link,
- Paste the link into a new window, much as a student would. Analysis, Defined Set, then click 000All at the top to highlight the superimposed chains. Once all is highlighted, toggle between the two states by clicking the Alternative (Key “a”) menu button directly under the File button.
- Now try View, Side by Side to see both (don’t toggle this form)