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salilab / IHMValidation

Validation software for integrative models deposited to PDB
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Some crosslinking-MS entries are missing atom labels in the `_ihm_cross_link_restraint` tables. #83

Open aozalevsky opened 2 months ago

aozalevsky commented 2 months ago

Here is one example (PDBDEV_00000089):

#                                                                                                                                                                                                                                                                                                                             
loop_                                                                                                                                                                                                                                                                                                                         
_ihm_cross_link_restraint.asym_id_1                                                                                                                                                                                                                                                                                           
_ihm_cross_link_restraint.asym_id_2                                                                                                                                                                                                                                                                                           
_ihm_cross_link_restraint.atom_id_1                                                                                                                                                                                                                                                                                           
_ihm_cross_link_restraint.atom_id_2                                                                                                                                                                                                                                                                                           
_ihm_cross_link_restraint.comp_id_1                                                                                                                                                                                                                                                                                           
_ihm_cross_link_restraint.comp_id_2                                                                                                                                                                                                                                                                                           
_ihm_cross_link_restraint.conditional_crosslink_flag                                                                                                                                                                                                                                                                          
_ihm_cross_link_restraint.distance_threshold                                                                                                                                                                                                                                                                                  
_ihm_cross_link_restraint.entity_id_1                                                                                                                                                                                                                                                                                         
_ihm_cross_link_restraint.entity_id_2                                                                                                                                                                                                                                                                                         
_ihm_cross_link_restraint.group_id                                                                                                                                                                                                                                                                                            
_ihm_cross_link_restraint.id                                                                                                                                                                                                                                                                                                  
_ihm_cross_link_restraint.model_granularity                                                                                                                                                                                                                                                                                   
_ihm_cross_link_restraint.pseudo_site_flag                                                                                                                                                                                                                                                                                    
_ihm_cross_link_restraint.psi                                                                                                                                                                                                                                                                                                 
_ihm_cross_link_restraint.restraint_type                                                                                                                                                                                                                                                                                      
_ihm_cross_link_restraint.seq_id_1                                                                                                                                                                                                                                                                                            
_ihm_cross_link_restraint.seq_id_2                                                                                                                                                                                                                                                                                            
_ihm_cross_link_restraint.sigma_1                                                                                                                                                                                                                                                                                             
_ihm_cross_link_restraint.sigma_2                                                                                                                                                                                                                                                                                             
A   B   .   .   GLU LYS ANY 3   1   1   1   1   by-atom No  .   harmonic    57  96  .   .                                                                                                                                                                                                                                     
B   A   .   .   GLU LYS ANY 3   1   1   1   2   by-atom No  .   harmonic    57  96  .   .                                                                                                                                                                                                                                     
A   B   .   .   GLU LYS ANY 3   1   1   2   3   by-atom No  .   harmonic    57  97  .   .                                                                                                                                                                                                                                     
B   A   .   .   GLU LYS ANY 3   1   1   2   4   by-atom No  .   harmonic    57  97  .   .                                                                                                                                                                                                                                     
A   B   .   .   GLU LYS ANY 3   1   1   3   5   by-atom No  .   harmonic    61  97  .   .                                                                                                                                                                                                                                     
B   A   .   .   GLU LYS ANY 3   1   1   3   6   by-atom No  .   harmonic    61  97  .   .                                                                                                                                                                                                                                     
A   B   .   .   LYS GLU ANY 3   1   1   4   7   by-atom No  .   harmonic    10  57  .   .                                                                                                                                                                                                                                     
B   A   .   .   LYS GLU ANY 3   1   1   4   8   by-atom No  .   harmonic    10  57  .   .                                                                                                                                                                                                                                     
A   B   .   .   GLU LYS ANY 3   1   1   5   9   by-atom No  .   harmonic    13  60  .   .                                                                                                                                                                                                                                     
B   A   .   .   GLU LYS ANY 3   1   1   5   10  by-atom No  .   harmonic    13  60  .   .                                                                                                                                                                                                                                     
A   B   .   .   GLU LYS ANY 3   1   1   6   11  by-atom No  .   harmonic    28  45  .   .                                                                                                                                                                                                                                     
B   A   .   .   GLU LYS ANY 3   1   1   6   12  by-atom No  .   harmonic    28  45  .   .

If the atomic restraint is missing the atom label, such restraint can't be properly assessed. I don't consider this a problem because the default behavior is to ignore any missing/incomplete data. I've noticed it only because "at a glance" plots were failing. I've added a workaround for reports.

The issue is just a note that we might want to address in the future. For instance, they can be updated to by-residue.

Here is a full list of affected entries: PDBDEV_00000089, PDBDEV_00000098, PDBDEV_00000203, PDBDEV_00000204, PDBDEV_00000205, PDBDEV_00000206, PDBDEV_00000207, PDBDEV_00000208

aozalevsky commented 2 months ago

@brindakv no action needed now, but we might want to update these entries in the future.

PDBDEV_00000089 is unclear from the paper. Modeling details are in the Appendix 01 https://www.pnas.org/doi/10.1073/pnas.2201910120#supplementary-materials

PDBDEV_00000098:

If a majority of structures in a cluster exhibit the inter-residue distance values within the Cα-Cα distance range the cross-linkers cover (BS3 with Cα-Cα distance <30 Å; DMTMM with Cα-Cα distance <16 Å),53

Seems like Ca-Ca (thus can be updated to by-residue), but entry has 30 and 10A thresholds, while the text says 30 and 16.

https://www.sciencedirect.com/science/article/pii/S0969212623000321?via%3Dihub

PDBDEV_0000020X series used Cb-Cb restraints:

The 136 hits from thiol trapping experiments representing pairs of receptor-arrestin positions at an estimated maximal Cβ-Cβ distance of about 10.2 Å (Fig. 2b) were translated into 136 soft harmonic restraints weighted by the corresponding crosslinking yields in an integrative modeling framework47,48,49.

https://www.nature.com/articles/s41467-023-36797-2

brindakv commented 1 month ago

Thanks @aozalevsky This can be addressed during remediation.