9A4C | pdb_00009a4c

Integrative model of ACP-HEPS2 by crosslinking MS and deep learning


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
ACP_BACSU77Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: acpA
UniProt
Find proteins for P80643 (Bacillus subtilis (strain 168))
Explore P80643 
Go to UniProtKB:  P80643
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80643
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HEPS2_BACSU348Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: hepT
EC: 2.5.1.30
UniProt
Find proteins for P31114 (Bacillus subtilis (strain 168))
Explore P31114 
Go to UniProtKB:  P31114
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31114
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