9A5C | pdb_00009a5c

Integrative model of GLPD-DNAD by crosslinking MS and deep learning

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.


Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Modelling protein complexes with crosslinking mass spectrometry and deep learning

Stahl, K.Warneke, R.Demann, L.Bremenkamp, R.Hormes, B.Brock, O.Stulke, J.Rappsilber, J.

(2024) Nat Commun 15: 7866

  • DOI: https://doi.org/10.1038/s41467-024-51771-2
  • Primary Citation of Related Structures:  
    9A40, 9A4A, 9A4B, 9A4C, 9A4D, 9A4E, 9A4F, 9A4G, 9A4H, 9A4I, 9A4J, 9A4K, 9A4L, 9A4M, 9A4N, 9A4O, 9A4P, 9A4Q, 9A4R, 9A4S, 9A4T, 9A4U, 9A4V, 9A4W, 9A4X, 9A4Y, 9A4Z, 9A50, 9A51, 9A52, 9A53, 9A54, 9A55, 9A56, 9A57, 9A58, 9A59, 9A5A, 9A5B, 9A5C, 9A5D, 9A5E, 9A5F, 9A5G, 9A5H, 9A5I, 9A5J, 9A5K, 9A5L, 9A5M

  • PubMed Abstract: 

    Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrate experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially improves modelling performance on challenging targets, by helping to identify interfaces, focusing sampling, and improving model selection. This extends to single crosslinks from whole-cell crosslinking MS, opening the possibility of whole-cell structural investigations driven by experimental data. We demonstrate this by revealing the molecular basis of iron homoeostasis in Bacillus subtilis.


  • Organizational Affiliation
    • Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLPD_BACSU555Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: glpD
EC: 1.1.5.3
UniProt
Find proteins for P18158 (Bacillus subtilis (strain 168))
Explore P18158 
Go to UniProtKB:  P18158
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18158
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNAD_BACSU232Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: dnaD
UniProt
Find proteins for P39787 (Bacillus subtilis (strain 168))
Explore P39787 
Go to UniProtKB:  P39787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39787
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release