9A9G | pdb_00009a9g

Biologically relevant conformational ensembles of the extracellular region of Streptococcus pneumoniae PsrSp

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/pdb9A9G/pdb

• Organism(s): Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
• Mutation(s): No 


• Deposited: 2025-01-24 Released: 2025-10-22 
• Deposition Author(s): Lesovoy, D., Sala, B.M., Sandalova, T., Achour, A., Orekhov, V., Roshchin, K., Agback, T., Agback, P.

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Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 20 
• Representative Model: 1 

Literature

Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation

Lesovoy, D., Roshchin, K., Sala, B.M., Sandalova, T., Achour, A., Agback, T., Agback, P., Orekhov, V.

(2025) Int J Mol Sci 26

• PubMed: 41009484 
• DOI: https://doi.org/10.3390/ijms26188917
• Primary Citation Related Structures: 
  9A9G


• PubMed Abstract: 
  

  Conformational heterogeneity is essential for protein function, yet validating theoretical molecular dynamics (MD) ensembles remains a significant challenge. In this study, we present an approach that integrates free MD simulations, starting from an AlphaFold-generated structure, with refined experimental NMR-relaxation data to identify biologically relevant holistic time-resolved 4D conformational ensembles. Specifically, we select trajectory segments (RMSD plateaus) consistent with experimental observables. For the extracellular region of Streptococcus pneumoniae PsrSp, we found that only specific segments of the long MD trajectory aligned well with experimental data. The resulting ensembles revealed two regions with increased flexibility, both of which play important functional roles.

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Organizational Affiliation: 
• Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia.
Science for Life Laboratory, Department of Medicine, Karolinska Institute, SE-171 65 Solna, Sweden.
Division of Infectious Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 465, SE-405 30 Gothenburg, Sweden.
Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden.
Swedish NMR Centre, University of Gothenburg, P.O. Box 465, SE-405 30 Gothenburg, Sweden.

Assembly  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Macromolecule Content 

• Total Structure Weight: 39.92 kDa 
• Atom Count: 2,417 
• Modeled Residue Count: 308 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LCP Protein PsrSp	A	308	Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	Mutation(s): 0
UniProt
Find proteins for Q8DPD6 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DPD6  Go to UniProtKB:  Q8DPD6

Experimental Data & Validation

Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 20 
• Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report

Entry History 

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Lesovoy, D., Sala, B.M., Sandalova, T., Achour, A., Orekhov, V., Roshchin, K., Agback, T., Agback, P.

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release