Talk:Schubert lab: bacterial InIC disrupts human Tuba complexes

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Scripts used

Fig 1A: Tuba-SH3 binds proline-rich peptides

load files "=4CC2" "=4CC3"
select all; cartoon only; cartoon off
select 1.1 and :A and protein; color green; spacefill only
select 1.1 and :B; trace only; color maroon; center selected
select 1.1 and :B and (sidechain or *.CA); wireframe 0.4
select 1.1 and :B and pro and (sidechain or *.N or *.CA); wireframe 0.4
select 2.1 and :B; trace only; color gold; trace 0.3
select 2.1 and :B and (sidechain or *.CA); wireframe 0.3
select 2.1 and :B and pro and (sidechain or *.N or *.CA); wireframe 0.3
model 0
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{1518-1573:A and not %B}{1518-1573:A and not *%B} ROTATE TRANSLATE 1.0
select 1.1 and :B and protein; dots on; set dotScale 2.0

1B NWASP: 4CC2

select all; cartoon only; cartoon off
select :A; cartoon; color green
select :B; cartoon; color maroon; cartoon only
SELECT 1530:A AND (SIDECHAIN OR *.CA); WIREFRAME 50 
SELECT 1530:A AND SIDECHAIN; COLOR GRAY 
SELECT (1554, 1570, 1522, 1524, 1567) AND :A and (sidechain or *.CA); WIREFRAME 50; 
select selected and not *.CA; COLOR BLUE
SELECT 1567:A and (sidechain or *.N or *.CA); WIREFRAME 50
select selected and not *.CA; COLOR BLUE
SELECT PRO:B and (sidechain or *.N or *.CA); WIREFRAME 50
SELECT :B and (sidechain or *.CA) and not pro; WIREFRAME 50
select 1550:A.CA; label “n-Src" 
select 1562:A.CA; label "4"
color label black

Fig. 2 InIC domains

load 4CC4
select all; cartoon only; cartoon off
select :A; cartoon; color skyblue
select :B; cartoon; color green
select (77-214) and :A; color purple
select (:A,:B) and protein
isosurface ignore (not selected) SASURFACE 1.2  MAP property color translucent 0.8

Fig 3b: Detailed view of InIC: Tuba interactions

select all; cartoon only; cartoon off
select (207-213, 185-191,163-169,142-148, 120-127) and :A; cartoon only; color slateblue
select (123, 125, 127, 166, 146, 168, 188, 210) and :A and (sidechain or *.CA); wireframe 0.4; color slateblue
select selected and sidechain and not _C; color cpk
select (1519-1523, 1568-1573) and :B; trace only; color limegreen
select (1572, 1570, 1522, 1569, 1521) and :B and (sidechain or *.CA); wireframe 0.4
select selected and sidechain and not _C; color cpk
select 1572:B%A; wireframe off
set zshade on
set zshadepower 4
set traceAlpha TRUE
set sheetSmoothing 0
select :A and (125.CB,123.CB,1570.CB,1522.CB,146.CB,127.CB,148.CB)
label "%m%r"
select :B and (1569.CB,168.CB,1572.CB,166.CB,188.CB,1521.CB,210.CB)
label "%m%r"

Fig 6a: InIC and NWASP would clash if bound to Tuba at the same time

cartoon only
console
select all; cartoon only; color skyblue
select :B; color green
select *:B/3
spacefill
frame 0
color red
frame 3
select :A/3
cartoon only
cartoon off
select :A/2
cartoon only
cartoon off
select none
select :B/3
isosurface ignore (not selected) SASURFACE 1.2 MAP property color

6B NWASP

load 4CC2
select all; cartoon only; cartoon off
select :A and protein; spacefill; color green
select (1572, 1552, 1521, 1573) and :A; color blue
select (1524, 1527, 1528, 1530, 1531, 1547-1549, 1554, 1565, 1567) and :A; color pink
select (1522, 1551, 1553, 1569, 1570) and :A; color silver
select :B; trace; color maroon
select :B and pro and (sidechain or *.N or *.CA); wireframe 0.3
select :B and not pro and (sidechain or *.CA); wireframe 0.3
select :A and protein; isosurface ignore (not selected) SASURFACE 1.2  MAP property