5FGS | pdb_00005fgs

Crystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG - P21212 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.250 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit

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

(2016) Sci Rep 6: 28664-28664

  • DOI: https://doi.org/10.1038/srep28664
  • Primary Citation Related Structures: 
    5F44, 5FAA, 5FGR, 5FGS, 5FIE, 5HBB, 5HDL, 5HTS, 5J4M

  • PubMed Abstract: 

    Thus far, all solved structures of pilin-proteins comprising sortase-assembled pili are from pathogenic genera and species. Here, we present the first crystal structure of a pilin subunit (SpaA) from a non-pathogen host (Lactobacillus rhamnosus GG). SpaA consists of two tandem CnaB-type domains, each with an isopeptide bond and E-box motif. Intriguingly, while the isopeptide bond in the N-terminal domain forms between lysine and asparagine, the one in the C-terminal domain atypically involves aspartate. We also solved crystal structures of mutant proteins where residues implicated in forming isopeptide bonds were replaced. Expectedly, the E-box-substituted E139A mutant lacks an isopeptide bond in the N-terminal domain. However, the C-terminal E269A substitution gave two structures; one of both domains with their isopeptide bonds present, and another of only the N-terminal domain, but with an unformed isopeptide bond and significant conformational changes. This latter crystal structure has never been observed for any other Gram-positive pilin. Notably, the C-terminal isopeptide bond still forms in D295N-substituted SpaA, irrespective of E269 being present or absent. Although E-box mutations affect SpaA proteolytic and thermal stability, a cumulative effect perturbing normal pilus polymerization was unobserved. A model showing the polymerized arrangement of SpaA within the SpaCBA pilus is proposed.


  • Organizational Affiliation
    • Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121 001, India.

Macromolecule Content 

  • Total Structure Weight: 59.81 kDa 
  • Atom Count: 3,993 
  • Modeled Residue Count: 493 
  • Deposited Residue Count: 544 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell surface protein SpaA
A, B, C, D
136Lacticaseibacillus rhamnosus GGMutation(s): 0 
Gene Names: LRHM_0426

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth D],
L [auth D],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.250 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.07α = 90
b = 74.343β = 90
c = 116.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building

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: 2016-07-20
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary