Chain_merge_symmetrization - I2PC/scipion-courses GitHub Wiki
Modeling workflow to built the structure of the asymmetric unit and the structure of the whole molecule of the human Hgb by applying symmetry (detailed in the general modeling workflow):
- Step 11a: Merging of chains A and B of human Hgb alpha and beta subunits, respectively, with ChimeraX operate protocol (details in modeling tutorial)
If you want to have HBA-refined and HBB_refined (red arrows 2 and 3, respectively) go for instructions to Fig. 13.2 of the modeling tutorial.
Once you have opened the ChimeraX GUI, merge the chains A and B and save the final asymmetric unit writing in the command line:
- scipioncombine #3,4
- scipionwrite #5 prefix asymmetric_unit_model_
- Step 12a: Manual flexible fitting with CCP4 Coot, if needed, in the overlapping area between chains A and B
- Step 13a: Automatic flexible fitting with Phenix Real space refine, if needed, in the overlapping area between chains A and B
- Step 14a: Building of the whole human Hgb molecule by applying symmetry to the asymmetric unit with ChimeraX operate protocol (details in modeling tutorial)
Once you have opened the ChimeraX GUI, apply symmetry, rename chains and save the whole structure as a unique model writing in the command line:
- sym #3 C2 copies true
Now change the names of chains in model #4.2
- sel #4.2/A
- changechains sel C
- sel #4.2/B
- changechains sel D
- combine #4
- scipionwrite #5 prefix whole_model_
- Step 15a: Manual flexible fitting with CCP4 Coot, if needed, in the overlapping area between asymmetric units
- Step 16a: Automatic flexible fitting with Phenix Real space refine, if needed, in the overlapping area between asymmetric units
Once we have the asymmetric unit or the whole macromolecule modeled, we can submit our map and model to databases.
Appendix
List of atom-atom interactions across protein-protein interface
---------------------------------------------------------------
PDB code: 5ni1 Chains A }{ B
------------------------------
Hydrogen bonds
--------------
<----- A T O M 1 -----> <----- A T O M 2 ----->
Atom Atom Res Res Atom Atom Res Res
no. name name no. Chain no. name name no. Chain Distance
1. 224 NH1 ARG 31 A <--> 2049 OE1 GLN 127 B 2.89
2. 225 NH2 ARG 31 A <--> 2006 O PHE 122 B 3.02
3. 782 NE2 HIS 103 A <--> 2081 NE2 GLN 131 B 2.99
4. 858 O PRO 114 A <--> 1959 NE2 HIS 116 B 2.75
5. 879 O PHE 117 A <--> 1292 NH2 ARG 30 B 2.94
6. 919 ND1 HIS 122 A <--> 1291 NH1 ARG 30 B 3.27
Non-bonded contacts
-------------------
<----- A T O M 1 -----> <----- A T O M 2 ----->
Atom Atom Res Res Atom Atom Res Res
no. name name no. Chain no. name name no. Chain Distance
1. 219 CB ARG 31 A <--> 2049 OE1 GLN 127 B 3.30
2. 220 CG ARG 31 A <--> 2049 OE1 GLN 127 B 3.09
3. 221 CD ARG 31 A <--> 2049 OE1 GLN 127 B 3.16
4. 223 CZ ARG 31 A <--> 2006 O PHE 122 B 3.82
5. 223 CZ ARG 31 A <--> 2049 OE1 GLN 127 B 3.83
6. 224 NH1 ARG 31 A <--> 2006 O PHE 122 B 3.69
7. 224 NH1 ARG 31 A <--> 2046 CB GLN 127 B 3.72
8. 224 NH1 ARG 31 A <--> 2048 CD GLN 127 B 3.74
9. 224 NH1 ARG 31 A <--> 2049 OE1 GLN 127 B 2.89
10. 225 NH2 ARG 31 A <--> 2006 O PHE 122 B 3.02
11. 251 CD1 LEU 34 A <--> 2025 CB PRO 124 B 3.42
12. 258 OG SER 35 A <--> 2048 CD GLN 127 B 3.78
13. 258 OG SER 35 A <--> 2050 NE2 GLN 127 B 3.74
14. 778 CG HIS 103 A <--> 1901 ND2 ASN 108 B 3.67
15. 779 ND1 HIS 103 A <--> 1898 CB ASN 108 B 3.88
16. 779 ND1 HIS 103 A <--> 1899 CG ASN 108 B 3.87
17. 779 ND1 HIS 103 A <--> 1901 ND2 ASN 108 B 3.37
18. 780 CD2 HIS 103 A <--> 2081 NE2 GLN 131 B 3.76
19. 781 CE1 HIS 103 A <--> 1897 O ASN 108 B 3.56
20. 781 CE1 HIS 103 A <--> 1898 CB ASN 108 B 3.61
21. 781 CE1 HIS 103 A <--> 1899 CG ASN 108 B 3.63
22. 781 CE1 HIS 103 A <--> 1901 ND2 ASN 108 B 3.55
23. 782 NE2 HIS 103 A <--> 2081 NE2 GLN 131 B 2.99
24. 811 CG2 VAL 107 A <--> 1929 SG CYS 112 B 3.86
25. 830 O ALA 110 A <--> 1948 O ALA 115 B 3.68
26. 830 O ALA 110 A <--> 1951 CA HIS 116 B 3.64
27. 833 CA ALA 111 A <--> 1948 O ALA 115 B 3.66
28. 835 O ALA 111 A <--> 1983 C GLY 119 B 3.89
29. 836 CB ALA 111 A <--> 1984 O GLY 119 B 3.62
30. 846 NE2 HIS 112 A <--> 1993 NZ LYS 120 B 3.77
31. 856 CA PRO 114 A <--> 1957 CD2 HIS 116 B 3.72
32. 856 CA PRO 114 A <--> 1959 NE2 HIS 116 B 3.71
33. 857 C PRO 114 A <--> 1959 NE2 HIS 116 B 3.58
34. 858 O PRO 114 A <--> 1957 CD2 HIS 116 B 3.59
35. 858 O PRO 114 A <--> 1958 CE1 HIS 116 B 3.77
36. 858 O PRO 114 A <--> 1959 NE2 HIS 116 B 2.75
37. 879 O PHE 117 A <--> 1290 CZ ARG 30 B 3.69
38. 879 O PHE 117 A <--> 1291 NH1 ARG 30 B 3.65
39. 879 O PHE 117 A <--> 1292 NH2 ARG 30 B 2.94
40. 889 C THR 118 A <--> 1291 NH1 ARG 30 B 3.65
41. 889 C THR 118 A <--> 1292 NH2 ARG 30 B 3.86
42. 890 O THR 118 A <--> 1291 NH1 ARG 30 B 3.79
43. 894 N PRO 119 A <--> 1290 CZ ARG 30 B 3.83
44. 894 N PRO 119 A <--> 1291 NH1 ARG 30 B 3.41
45. 894 N PRO 119 A <--> 1292 NH2 ARG 30 B 3.63
46. 895 CA PRO 119 A <--> 1291 NH1 ARG 30 B 3.37
47. 899 CG PRO 119 A <--> 1290 CZ ARG 30 B 3.84
48. 899 CG PRO 119 A <--> 1292 NH2 ARG 30 B 3.82
49. 899 CG PRO 119 A <--> 1498 CE MET 55 B 3.35
50. 900 CD PRO 119 A <--> 1290 CZ ARG 30 B 3.85
51. 900 CD PRO 119 A <--> 1292 NH2 ARG 30 B 3.40
52. 917 CB HIS 122 A <--> 1291 NH1 ARG 30 B 3.39
53. 918 CG HIS 122 A <--> 1291 NH1 ARG 30 B 3.78
54. 918 CG HIS 122 A <--> 1322 CG2 VAL 34 B 3.89
55. 919 ND1 HIS 122 A <--> 1288 CD ARG 30 B 3.75
56. 919 ND1 HIS 122 A <--> 1291 NH1 ARG 30 B 3.27
57. 948 OD1 ASP 126 A <--> 1334 OH TYR 35 B 3.51
Number of hydrogen bonds: 6
Number of non-bonded contacts: 57
List of atom-atom interactions across protein-protein interface
---------------------------------------------------------------
PDB code: 5ni1 Chains A }{ C
------------------------------
Hydrogen bonds
--------------
<----- A T O M 1 -----> <----- A T O M 2 ----->
Atom Atom Res Res Atom Atom Res Res
no. name name no. Chain no. name name no. Chain Distance
1. 1 N VAL 1 A <--> 3229 OG SER 138 C 2.81
2. 1036 OG SER 138 A <--> 2195 N VAL 1 C 2.82
Non-bonded contacts
-------------------
<----- A T O M 1 -----> <----- A T O M 2 ----->
Atom Atom Res Res Atom Atom Res Res
no. name name no. Chain no. name name no. Chain Distance
1. 1 N VAL 1 A <--> 3228 CB SER 138 C 3.26
2. 1 N VAL 1 A <--> 3229 OG SER 138 C 2.81
3. 20 CB SER 3 A <--> 3233 O LYS 139 C 3.80
4. 958 NZ LYS 127 A <--> 3233 O LYS 139 C 3.69
5. 1035 CB SER 138 A <--> 2195 N VAL 1 C 3.26
6. 1036 OG SER 138 A <--> 2195 N VAL 1 C 2.82
7. 1040 O LYS 139 A <--> 2214 CB SER 3 C 3.80
8. 1040 O LYS 139 A <--> 3151 NZ LYS 127 C 3.70
Number of hydrogen bonds: 2
Number of non-bonded contacts: 8