9A5E | pdb_00009a5e

Integrative model of DPO41-RPOZ 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.

• PDB DOI: https://doi.org/10.2210/pdb9A5E/pdbIHM Entry Collection: PDBDEV_G_1000003

• Organism(s): Bacillus subtilis (strain 168)
• Mutation(s): No 


• Deposited: 2024-01-23 Released: 2024-09-18 
• Deposition Author(s): Stahl, K., Brock, O., Rappsilber, J.

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Integrative Structure Snapshot

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

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

• PubMed: 39251624 
• DOI: https://doi.org/10.1038/s41467-024-51771-2
• Primary Citation 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, ... Search all related entries


• 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.

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Organizational Affiliation: 
• Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany.
Georg-August-Universität Göttingen, Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Göttingen, Germany.
Technische Universität Berlin, Robotics and Biology Laboratory, Berlin, Germany.
Science of Intelligence, Research Cluster of Excellence, Berlin, Germany.
Georg-August-Universität Göttingen, Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Göttingen, Germany. [e-mail].
Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany. [e-mail].
Si-M/"Der Simulierte Mensch", a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany. [e-mail].
Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. [e-mail].

Assembly  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Macromolecule Content 

• Total Structure Weight: 63.48 kDa 
• Atom Count: 3,845 
• Modeled Residue Count: 481 
• Deposited Residue Count: 481 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DPO41_BACSU	A	414	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: dinB1 EC: 2.7.7.7
UniProt
Find proteins for P54545 (Bacillus subtilis (strain 168)) Explore P54545  Go to UniProtKB:  P54545

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RPOZ_BACSU	B	67	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: rpoZ EC: 2.7.7.6
UniProt
Find proteins for O35011 (Bacillus subtilis (strain 168)) Explore O35011  Go to UniProtKB:  O35011

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

• Released Date: 2024-09-18 
Deposition Author(s): Stahl, K., Brock, O., Rappsilber, J.

Revision History  

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