9A2V | pdb_00009a2v

Model of E. coli AcrA by in-cell photo-crosslinking MS and deep learning


Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 10 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

Stahl, K.Graziadei, A.Dau, T.Brock, O.Rappsilber, J.

(2023) Nature Biotechnology 

  • DOI: https://doi.org/10.1038/s41587-023-01704-z
  • Primary Citation of Related Structures:  
    9A2G, 9A2H, 9A2I, 9A2J, 9A2K, 9A2L, 9A2M, 9A2N, 9A2O, 9A2P, 9A2Q, 9A2R, 9A2S, 9A2T, 9A2U, 9A2V, 9A2W, 9A2X, 9A2Y, 9A2Z, 9A30, 9A31, 9A32, 9A33, 9A34, 9A35, 9A36, 9A37, 9A38, 9A39, 9A3A, 9A3B, 9A3C, 9A3D

  • PubMed Abstract: 

    While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its network architecture. By employing sparse experimental contacts as anchor points, AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets. We confirm this experimentally by using the noncanonical amino acid photo-leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. The program can predict distinct conformations of proteins on the basis of the distance restraints provided, demonstrating the value of experimental data in driving protein structure prediction. The noise-tolerant framework for integrating data in protein structure prediction presented here opens a path to accurate characterization of protein structures from in-cell data.


  • Organizational Affiliation
    • Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P0AE06397Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acrA
UniProt
Find proteins for P0AE06 (Escherichia coli (strain K12))
Explore P0AE06 
Go to UniProtKB:  P0AE06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE06
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 10 
  • 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: 2023-02-24
    Type: Initial release