Talk:Schubert lab: bacterial InIC disrupts human Tuba complexes

From Proteopedia

Scripts used

All of the scripts make use of the same uploaded coordinate file, Tuba-3.pdb. The advantage is that the scene transitions are smooth, and no additional coordinates have to be loaded. The disadvantage is the atom selection in the scripts is a bit more convoluted.

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

select all; cartoon only; cartoon off
select :B/2 and protein; color green; spacefill only
select :C/2; trace only; color maroon; center selected
select :C/2 and (sidechain or *.CA); wireframe 0.4
select :C/2 and pro and (sidechain or *.N or *.CA); wireframe 0.4
select :C/3; trace only; color gold; trace 0.3
select :C/3 and (sidechain or *.CA); wireframe 0.3
select :C/3 and pro and (sidechain or *.N or *.CA); wireframe 0.3
model 0
select :C/2 and protein; dots on;

Fig 1B: Details of Tuba N-WASP interactions

The labels had to be done one by one because the residue numbers in the PDB file and in the publication were off by one.

select all; cartoon only; cartoon off
select :B; cartoon; color green
select :C; cartoon; color maroon; cartoon only
select :C/3; color gold
SELECT (1554, 1570, 1522, 1524, 1567) AND :B and (sidechain or *.CA); WIREFRAME 50; 
select selected and not *.CA; COLOR BLUE
SELECT 1567:B and (sidechain or *.N or *.CA); WIREFRAME 50
select selected and not *.CA; COLOR BLUE
SELECT PRO:C and (sidechain or *.N or *.CA); WIREFRAME 50
SELECT :C and (sidechain or *.CA) and not pro; WIREFRAME 50
SELECT (1530,1565, 1547,1548,1569,1553) AND :B and (sidechain or *.CA); WIREFRAME 50; 
select selected and not *.CA; COLOR gray
set fontScaling ON
select 1550:B.CA; label “n-Src"
select 1562:B.CA; label "4"
select 1551:B.CZ2; label "W1554"
select 1554:B.CE2; label "W1554"
select 1567:B.CA; label "P1567" ; color label blue 
select 1524:B.CD2; label "F1524"; color label blue
select 1570:B.OH; label "Y1570"; color label blue
select 1552:B.CD1; label "Y1552"; color label blue
select 1522:B.CD1; label "Y1522"; color label blue
select 13:C.CA/2; label "G12"; color label red
select 12:C.OG/2; label "S11"; color label red
select 11:C.CA/2; label "P10"; color label red
select 10:C.CA/2; label "A9"; color label red
select 9:C.CB/2; label "S8"; color label red
select 8:C.OG/2; label "S7"; color label red
select 7:C.CB/2; label "P6"; color label red
select 6:C.CG/2; label "L5"; color label red
select 5:C.CB/2; label "A4"; color label red
select 4:C.CB/2; label "P3"; color label red
select 3:C.CB/2; label "P2"; color label red
select 2:C.CD/2; label "P1"; color label red
select 1537:B.CA; label "RT-Src"; color label green
select 1559:B.CA; label "3"; color label black
select 1540:B.CA; label "2"; color label black
select 1530:B.CB; label "N1530"; color label gray
SELECT (1530,1565, 1547,1548,1569,1553) AND :B and (sidechain or *.CA); WIREFRAME 50
select selected and not *.CA; COLOR gray
select 1565:B.CE2; label "Y1565"; color label gray
select 1548:B.CG1; label "V1548"; color label gray
select 1547:B.CG; label "D1547"; color label gray
select 1553:B.CD; label "E1553"; color label gray
select 1569:B.ND2%A; label "N1569"; color label gray
select 1520:B.CA; label "1"; color label black
select 1562:B.CA; label "4"; color label black
select 1569:B.CA; label "3_10"; color label black
select all; set fontSize 7

Fig. 2 InIC domains

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/1,:B/1) and protein
select 131.cb
label "LRR"; color label purple
select [ASN]297:A.CA #2126 14.519 26.754 61.491
Label "Ig-like"; color label blue
select [THR]66:A.CA #248 -4.249 -6.123 16.996
label "Cap"; color label blue
select [GLY]1561:B.CA/1 #2556 14.293 32.833 2.076
label "SH3"
select [PRO]1529:B.CA/1 #2281 7.436 17.183 2.841
label "Tuba SH3-6"
model 1
isosurface ignore (not selected) SASURFACE 1.2  MAP property color translucent 0.8

Fig 3b: Detailed view of InIC: Tuba interactions

set fontScaling ON
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
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"
model 1

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

select all; cartoon only; color skyblue
select (77-214) and :A/1; color purple
select :B; color green
select :C/3 and protein; spacefill; color red
select :B/3; cartoon only; cartoon off
select :B/2; cartoon only; cartoon off
#select :B/3 and protein; 
#isosurface ignore (not selected) SASURFACE 1.2 MAP property color

Fig 6b: Interactions color-coded on Tuba SH3-6 domain

select all; cartoon only; cartoon off
select :B/2 and protein; spacefill; color green
select (1572, 1552, 1521, 1573) and :B/2; color blue
select (1524, 1527, 1528, 1530, 1531, 1547-1549, 1554, 1565, 1567) and :B/2; color pink
select (1522, 1551, 1553, 1569, 1570) and :B/2; color silver
select :C/2; trace; color maroon
select :C/2 and pro and (sidechain or *.N or *.CA); wireframe 0.3
select :C/2 and not pro and (sidechain or *.CA); wireframe 0.3

select :B/2 and protein; 
isosurface ignore (not selected) SASURFACE 1.2  MAP property

Fig. X (bonus figure)

select all; cartoon only; cartoon off
select :B/2 and protein; color green; trace
select :B/3 and protein; color lawngreen; trace
select :C/2; trace only; color maroon; center selected
select :C/2 and (sidechain or *.CA); wireframe 0.4
select :C/2 and pro and (sidechain or *.N or *.CA); wireframe 0.4
select :C/3; trace only; color gold; trace 0.3
select :C/3 and (sidechain or *.CA); wireframe 0.3
select :C/3 and pro and (sidechain or *.N or *.CA); wireframe 0.3
model 0
compare {*/3} {*/1} SUBSET{*.CA} ATOMS{1518-1520:B/3}{64-66:A/1} ROTATE TRANSLATE

Superpose button:

compare {*/3} {*/2} SUBSET{*.CA} ATOMS{1518-1573:B/3}{1518-1573:B/2} ROTATE TRANSLATE 2.0

Separate button:

compare {*/3} {*/1} SUBSET{*.CA} ATOMS{1518-1520:B/3}{64-66:A/1} ROTATE TRANSLATE 2.0