Crystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG in bent conformation

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

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Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism.

Chaurasia, P.Pratap, S.Palva, A.von Ossowski, I.Krishnan, V.

(2018) Commun Biol 1: 94-94

  • DOI: https://doi.org/10.1038/s42003-018-0100-0
  • Primary Citation of Related Structures:  
    5YU5, 5YXG, 5YXO, 5Z0Z, 5Z24

  • PubMed Abstract: 

    Effective colonization of host cells by some Gram-positive bacteria often involves using lengthy, adhesive macromolecular structures called sortase-dependent pili. Among commensals, the gut-adapted Lactobacillus rhamnosus GG strain encodes the operons for two varieties of these pili (SpaCBA and SpaFED), with each structure consisting of backbone, tip, and basal pilin subunits. Although the tertiary structure was recently solved for the backbone subunit (SpaA) of the SpaCBA pilus, no structural information exists for its counterpart in the SpaFED pilus. Here, we report several crystal structures for the SpaD backbone pilin, two of which capture the N-terminal domain in either the closed (linear) or open (bent) conformation. To our knowledge, this is the first observation of the bent conformation in Gram-positive pilin structures. Based on this bent conformation, we suggest a three-stage model, which we call the expose-ligate-seal mechanism, for the docking and assembly of backbone pilins into the sortase-dependent pilus.

  • Organizational Affiliation

    Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pilus assembly protein465Lacticaseibacillus rhamnosus GGMutation(s): 0 
Gene Names: CCE29_10230PY66_09460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.72α = 90
b = 73.72β = 90
c = 428.659γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of BiotechnologyIndiaBT/PR5891/BRB/10/1098/2012

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description