## 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