8W5B | pdb_00008w5b

Crystal Structure of the shaft pilin LrpA from Ligilactobacillus ruminis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.240 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Models: experimental, in silico
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Literature

The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis.

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

(2024) Acta Crystallogr D Struct Biol 80: 474-492

  • DOI: https://doi.org/10.1107/S2059798324005114
  • Primary Citation Related Structures: 
    8KB2, 8KCL, 8KG4, 8W5B, 8WB8

  • PubMed Abstract: 

    Sortase-dependent pili are long surface appendages that mediate attachment, colonization and biofilm formation in certain genera and species of Gram-positive bacteria. Ligilactobacillus ruminis is an autochthonous gut commensal that relies on sortase-dependent LrpCBA pili for host adherence and persistence. X-ray crystal structure snapshots of the backbone pilin LrpA were captured in two atypical bent conformations leading to a zigzag morphology in the LrpCBA pilus structure. Small-angle X-ray scattering and structural analysis revealed that LrpA also adopts the typical linear conformation, resulting in an elongated pilus morphology. Various conformational analyses and biophysical experiments helped to demonstrate that a hinge region located at the end of the flexible N-terminal domain of LrpA facilitates a new closure-and-twist motion for assembling dynamic pili during the assembly process and host attachment. Further, the incongruent combination of flexible domain-driven conformational dynamics and rigid isopeptide bond-driven stability observed in the LrpCBA pilus might also extend to the sortase-dependent pili of other bacteria colonizing a host.


  • Organizational Affiliation
    • Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR, Biotech Science Cluster, Faridabad 121 001, India.

Macromolecule Content 

  • Total Structure Weight: 49.34 kDa 
  • Atom Count: 3,050 
  • Modeled Residue Count: 404 
  • Deposited Residue Count: 455 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LPXTG-motif cell wall anchor domain protein455Ligilactobacillus ruminis ATCC 25644Mutation(s): 0 
Gene Names: HMPREF0542_11612
UniProt
Find proteins for E7FRT5 (Ligilactobacillus ruminis ATCC 25644)
Explore E7FRT5 
Go to UniProtKB:  E7FRT5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7FRT5
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.240 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.391α = 90
b = 47.391β = 90
c = 227.411γ = 120
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/PR22343/BRB/10/1570/2016

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references