RNA polymerase II complex of S. cerevisiae
This example utilizes the RNA polymerase II complex of S. cerevisiae (1WCM, chain A and E) for which 6 BS3 cross-links were available (Chen et al., 2010; Kahraman et al., 2013). The allowed distance was set between 0 and 30 Å (Cβ – Cβ) for every restraint. Two false-positive restraints were added with a distance in the crystal structure of 35.7 (FP1) and 42.2 Å (FP2) to test whether they could be identified. For the setup of the run, the "Complete scanning" option was selected and a selection for the interface analysis was provided specifying 10 residues for each the fixed and the scanning chain. Applying DisVis shows that none of the 2.7 x 10^9 complexes sampled are consistent with all 8 restraints, though a small number are conforming to 7 cross-links (2037 complexes). For the latter, only restraint FP2 is violated. The accessible interaction space consistent with at least 6 restraints is less than 0.03% of the full interaction space . The density clearly indicates the position of the E-chain. Interestingly, both false-positive restraints are violated in over 99% of the complexes consistent with at least six restraints; in contrast, the highest violation percentage of a correct cross-link is only 0.1%. Thus, a high-violation percentage is an indication of a false-positive restraint.
Run Example1
Status: FINISHED
Your DisVis run has successfully completed.
| Archive of the complete run: | Example1.tgz |
| Archive of all autogenerated images: | In preparation... |
- R.V. Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin (2021). Structural biology in the clouds: The WeNMR-EOSC Ecosystem. Frontiers Mol. Biosci., 8, fmolb.2021.729513.
- G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin (2016)
The DisVis and PowerFit web servers: Explorative and Integrative
Modeling of Biomolecular Complexes.
J. Mol. Biol., Advanced Online Publication. - G.C.P. van Zundert and A.M.J.J. Bonvin (2015) DisVis: Quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes." Bioinformatics 31, 3222-3224.
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Accessible Interaction Space
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Accessible Complexes
The table below lists the number of complexes consistent with at least N restraints as raw number and as fraction of all complexes.
| Number of consistent restraints (N) | Number of accessible complexes consistent with at least N restraints | Fraction of accessible complexes consistent with at least N restraints |
|---|---|---|
| 0 | 2728804709 | 100.00 % |
| 1 | 351952997 | 12.90 % |
| 2 | 145379581 | 5.33 % |
| 3 | 44726037 | 1.64 % |
| 4 | 13849208 | 0.51 % |
| 5 | 2730966 | 0.10 % |
| 6 | 818148 | 0.03 % |
| 7 | 2037 | 0.00 % |
| 8 | 0 | 0.00 % |
z-Score
The table below features the z-Score for each restraint. The higher the score, the more likely the restraint is a false-positive. Z-scores above 1.0 are explicitly mentioned in the output of DisVis.
| # | Restraint | Average violated fraction | Standard deviation | Z-score |
|---|---|---|---|---|
| 1 | A1003(CB)-E166(CB) | 0.26 | 0.30 | -0.79 |
| 2 | A129(CB)-E161(CB) | 0.30 | 0.29 | -0.65 |
| 3 | A129(CB)-E171(CB) | 0.24 | 0.30 | -0.85 |
| 4 | A15(CB)-E171(CB) | 0.37 | 0.30 | -0.38 |
| 5 | A934(CB)-E201(CB) | 0.39 | 0.30 | -0.29 |
| 6 | A938(CB)-E201(CB) | 0.36 | 0.31 | -0.38 |
| 7 | A180(CB)-E122(CB) | 0.80 | 0.33 | 1.29 |
| 8 | A1092(CB)-E152(CB) | 1.00 | 0.01 | 2.05 |
Violations
The table below shows how often a specific restraint is violated for complexes consistent with a number of restraints. The higher the violation fraction of a specific restraint, the more likely it is to be a false-positive. Column 1 shows the number of consistent restraints N, while each following column indicates the violation fractions of a specific restraint for complexes consistent with at least N restraints. Each row thus represents the fraction of all complexes consistent with at least N restraints that violated a particular restraint.
| Number of consistent restraints (N) | Restraint 1 | Restraint 2 | Restraint 3 | Restraint 4 | Restraint 5 | Restraint 6 | Restraint 7 | Restraint 8 |
|---|---|---|---|---|---|---|---|---|
| 1 | 0.73 | 0.81 | 0.78 | 0.81 | 0.74 | 0.78 | 0.77 | 0.98 |
| 2 | 0.68 | 0.62 | 0.59 | 0.72 | 0.50 | 0.50 | 0.97 | 1.00 |
| 3 | 0.31 | 0.35 | 0.29 | 0.43 | 0.65 | 0.62 | 0.97 | 1.00 |
| 4 | 0.08 | 0.15 | 0.06 | 0.24 | 0.65 | 0.60 | 0.96 | 1.00 |
| 5 | 0.02 | 0.14 | 0.00 | 0.36 | 0.18 | 0.06 | 0.94 | 1.00 |
| 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 |
| 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 |
Interaction analysis
The tables below shows how often a selected residues of the fixed and scanning chain are involved in the interaction in the complexes consistent with a specific number of restraints. The higher the interaction fraction of a specific residue is, the more likely it is involved in the complex interaction. Column 1 shows the residue ID, while each following column indicates the minimum number of restraints N. Each row thus represents the frequency that a residue of the receptor is found at the interface in complexes that are consistent with at least N restraints.
| 5 | 6 | 7 | 8 | |
|---|---|---|---|---|
| 161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 861 | 0.008 | 0.007 | 0.000 | 0.000 |
| 862 | 0.007 | 0.011 | 0.003 | 0.000 |
| 863 | 0.006 | 0.014 | 0.004 | 0.000 |
| 864 | 0.001 | 0.003 | 0.001 | 0.000 |
| 865 | 0.001 | 0.002 | 0.000 | 0.000 |
| 5 | 6 | 7 | 8 | |
|---|---|---|---|---|
| 46 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | 0.000 | 0.000 | 0.000 | 0.000 |
| 146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 148 | 0.003 | 0.003 | 0.000 | 0.000 |
| 149 | 0.016 | 0.027 | 0.008 | 0.000 |
| 150 | 0.003 | 0.006 | 0.000 | 0.000 |
