9RPL | pdb_00009rpl

Lactobacillus acidophilus SlpA self assembly domains I-II (aa 49-308)

• PDB DOI: https://doi.org/10.2210/pdb9RPL/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Lactobacillus acidophilus NCFM
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-25 Released: 2026-02-04 
• Deposition Author(s): Grininger, C., Pavkov-Keller, T.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Models: experimental

Literature

Guiding AlphaFold predictions with experimental knowledge to inform dynamics and interactions with VAIRO.

Trivino, J., Jimenez, E., Grininger, C., Caballero, I., Medina, A., Castellvi, A., Petrillo, G., Govantes, F., Sagmeister, T., Alcorlo, M., Hermoso, J.A., Sammito, M.D., Diederichs, K., Pavkov-Keller, T., Uson, I.

(2026) Protein Sci 35: e70481-e70481

• PubMed: 41578971 
• DOI: https://doi.org/10.1002/pro.70481
• Primary Citation Related Structures: 
  9RPL


• PubMed Abstract: 
  

  Structural predictions have reached unprecedented accuracy. They leverage sequence-specific data to capture all potential interactions a sequence has evolved to fulfill. AlphaFold derives information from three sources: learned parameters capturing intrinsic amino acid secondary structure and environment propensity; models of related proteins providing structural templates; and aligned sequences encoding profiles and concerted evolutionary changes of residues involved in contacts. However, function demands dynamic changes; hence not all possible interactions can coexist simultaneously. Comprehensive information entails contradictions, which resolved in favor of the better-informed structure will silence less stable states and associations. Here, we introduce a method using all three channels to include prior knowledge: site-specific variants, predefined alignments and templates. Selecting information relevant to a particular state delimits the functional context of a prediction. Our program VAIRO allows us to rescue asymmetric and weaker interactions to complete the view of molecular assemblies in the architecture of a bacterial surface layer, and reveals otherwise inaccessible dynamic states in a pneumococcal multimeric membrane protein complex. VAIRO is distributed via the python package index (PyPI) (https://pypi.org/project/vairo) and the code is also available on Github (https://github.com/arcimboldo-team/vairo).

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Organizational Affiliation: 
• Department of Structural Biology, Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain.
Facultad de Farmacia, Universidad de Barcelona, Barcelona, Spain.
Institute of Molecular Biosciences, University of Graz, Graz, Austria.
Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain.
Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain.
Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera (IQF-CSIC), Madrid, Spain.
Fachbereich Biologie, Universität Konstanz, Constance, Germany.
Field of Excellence BioHealth, University of Graz, Graz, Austria.
BioTechMed-Graz, Graz, Austria.
ICREA: Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 56.32 kDa 
• Atom Count: 4,074 
• Modeled Residue Count: 523 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-layer protein	A, B	270	Lactobacillus acidophilus NCFM	Mutation(s): 0  Gene Names: slpA, LBA0169
UniProt
Find proteins for P35829 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore P35829  Go to UniProtKB:  P35829

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	D [auth A], E [auth B], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.069	α = 90
b = 50.559	β = 113.94
c = 118.638	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Grininger, C., Pavkov-Keller, T.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	DOC 130

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release