6M7C | pdb_00006m7c

Crystal structure of C-terminal fragment of pilus adhesin SpaC from Lactobacillus rhamnosus GG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 
    0.318 (Depositor), 0.315 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.276 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili.

Kant, A.Palva, A.von Ossowski, I.Krishnan, V.

(2020) J Struct Biol 211: 107571-107571

  • DOI: https://doi.org/10.1016/j.jsb.2020.107571
  • Primary Citation Related Structures: 
    6M3Y, 6M48, 6M7C, 7BVX

  • PubMed Abstract: 

    Adhesion to cell surfaces is an essential and early prerequisite for successful host colonization by bacteria, and in most instances involves the specificities of various adhesins. Among bacterial Gram-positives, some genera and species mediate attachment to host cells by using long non-flagellar appendages called sortase-dependent pili. A case in point is the beneficial Lactobacillus rhamnosus GG gut-adapted strain that produces the so-called SpaCBA pilus, a structure noted for its promiscuous binding to intestinal mucus and collagen. Structurally, SpaCBA pili are heteropolymers of three different pilin-protein subunits, each with its own location and function in the pilus: backbone SpaA for length, basal SpaB for anchoring, and tip SpaC for adhesion. Previously, we solved the SpaA tertiary structure by X-ray crystallography and also reported on the crystallization of SpaB and SpaC. Here, we reveal the full-length high-resolution (1.9 Å) crystal structure of SpaC, a first for a sortase-dependent pilus-bearing commensal. The SpaC structure, unlike the representative four-domain architecture of other Gram-positive tip pilins, espouses an atypically longer five-domain arrangement that includes N-terminal 'binding' and C-terminal 'stalk' regions of two and three domains, respectively. With the prospect of establishing new mechanistic insights, we provide a structural basis for the multi-substrate binding nature of SpaC, as well as a structural model that reconciles its exclusive localization at the SpaCBA pilus tip.


  • Organizational Affiliation
    • Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 122016, India; Department of Biotechnology, Manipal University, Karnataka 576104, India.

Macromolecule Content 

  • Total Structure Weight: 29.35 kDa 
  • Atom Count: 1,673 
  • Modeled Residue Count: 262 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pilus assembly protein272Lacticaseibacillus rhamnosusMutation(s): 0 
Gene Names: CCE29_04955

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free:  0.318 (Depositor), 0.315 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.276 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.244α = 90
b = 58.559β = 90
c = 166.764γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR5891/BRB/10/1098/2012

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Structure summary
  • Version 1.3: 2020-09-09
    Changes: Structure summary
  • Version 1.4: 2021-09-15
    Changes: Advisory, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-11-06
    Changes: Structure summary