Rous sarcoma virus capsid compared to HIV

Thu Apr 7 17:48 PDT 2011

1

Opened emd_1862.map (#0), size 2553, grid spacing 1.27 Å
contour level -363, minimum -17270, maximum 14818
mean -6649.5, sd 3176.6, rms 7369.3, 16-bit integer
2

Opened 1em9.pdb (#1), 2 chains A B, 2257 atoms, x-ray 2.05 Angstroms
rous sarcoma virus capsid protein: n-terminal domain
weight 30.04 KDa

3 Deleted 1091 atoms (chain B), 1em9.pdb (#1)
4

Opened 1eoq.pdb (#2), 1 chain A, 1209 atoms, NMR
rous sarcoma virus capsid protein: c-terminal domain
weight 8.497 KDa

5 Molecular weight 24.04 KDa, 2375 atoms (1em9.pdb (#1), 1eoq.pdb (#2)).
6 Contour level 1239, emd_1862.map (#0)
7 Enclosed volume 1.78e6 Å3, area 454.6e3 Å3, emd_1862.map (#0)
8 Note: Set contour level to enclose volume 60 * 24 KDa * 1.2 Å3/Da
9

Fit 1em9.pdb (#1) in emd_1862.map (#0)
correlation 0.7883, average density 4850, 173 of 1166 atoms outside contour
simulated map 10.4 Å, envelope 0.95 mass enclosed, optimized overlap

rock movie
session9.py
10

Segmented emd_1862.map (#0)
regions 360, smoothing steps 3, step size 1 voxel

11

Segmentation grouping emd_1862.map (#0)
regions 120, smoothing level 4 voxels

12

Fit to segment 1eoq.pdb (#2) in region 1966, emd_1862.seg (#3)
correlation 0.8737, masked to region
simulated map 10.4 Å, envelope 0.95 mass enclosed, optimized overlap

13

Spin movie 1em9.pdb (#1), 1eoq.pdb (#2), emd_1862.seg (#3)

spin session13.py
14

Combined 1em9.pdb (#1), 1eoq.pdb (#2) producing combination (#4)

15

Saved ca_fit.pdb (#4) relative to emd_1862.map (#0).

16

Symmetry copies ca_fit.pdb (#4) producing (#5.1-59)
icosahedral 222r, coordinate system emd_1862.map (#0).

17

Simulated map ca_fit.pdb (#4), (#5.1-59) producing molmap res 10.4 (#6)
resolution 10.4, grid spacing 1.27 Å

 session17.py
18

Saved map ca_fit_60_r10.4.mrc (#6)

19

Measure correlation ca_fit_60_r10.4.mrc (#6), emd_1862.map (#0).
corr 0.9403, corr about mean 0.6705, within contour level 0.19 (#6).

20

Resampled map ca_fit_60_r10.4.mrc (#6) on grid emd_1862.map (#0) producing (#7).

21

Saved map ca_fit.mrc (#7).

22

Shifted map emd_1862.map (#0) by 6649 producing (#9).

23

Scaled map (#9) by 2.63e-5 producing map (#10).

24

Saved map emd_1862_normal.mrc (#10)

25

Morph maps emd_1862_normal.mrc (#10) to ca_fit.mrc (#7)
producing map (#11).

morph25.mov
26

Difference map ca_fit.mrc (#7), emd_1862_normal.mrc (#10).
Minimum RMS scaling. Contours -0.19 blue, 0.19 red.

spin26.mov
27

Note: 2 pentamers

 session26.py
28

Molecular surfaces ca_fit.pdb (#4), (#5.1)

 rock28.mov
29

Buried area ca_fit.pdb (#4), (#5.1)
solvent accessible area 486.4 Å2, solvent excluded area 138.0 Å2.

29

Buried residues ca_fit.pdb (#4), (#5.1)
11 residues, solvent accessible area cutoff 10 Å2.
Total buried SAS area 303.0 Å2, average 27.5 Å2.

residue list
30

Opened 3p05.pdb (#12), x-ray 2.50 Angstroms
5 chains A B C D E, 7918 atoms, 1043 residues
pentameric hiv-1 ca
weight 105 KDa

31

Fit 3p05.pdb (#12) in emd_1862.map (#0)
correlation 0.53, average density 3548, 2160 of 7918 atoms outside contour
simulated map 10.4 Å, envelope 0.95 mass enclosed, optimized overlap

32

Note: Superposition of HIV and RSV pentamers.
HIV 3p05.pdb (light blue and pink)
RSV ca_fit.pdb (blue and red)
Helices align. HIV squeezed toward center.

spin32.mov
session32.py

Fri Apr 8 00:15 PDT 2011