2Y1V

Full length structure of RrgB Pilus protein from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Full-Length Streptococcus Pneumoniae Major Pilin Rrgb Crystallizes in a Fibre-Like Structure, which Presents the D1 Isopeptide Bond and Provides Details on the Mechanism of Pilus Polymerization.

El Mortaji, L.Contreras-Martel, C.Moschioni, M.Ferlenghi, I.Manzano, C.Vernet, T.Dessen, A.Di Guilmi, A.M.

(2012) Biochem J 441: 833

  • DOI: https://doi.org/10.1042/BJ20111397
  • Primary Citation of Related Structures:  
    2Y1V

  • PubMed Abstract: 

    RrgB is the major pilin which forms the pneumococcal pilus backbone. We report the high-resolution crystal structure of the full-length form of RrgB containing the IPQTG sorting motif. The RrgB fold is organized into four distinct domains, D1-D4, each of which is stabilized by an isopeptide bond. Crystal packing revealed a head-to-tail organization involving the interaction of the IPQTG motif into the D1 domain of two successive RrgB monomers. This fibrillar assembly, which fits into the electron microscopy density map of the native pilus, probably induces the formation of the D1 isopeptide bond as observed for the first time in the present study, since neither in published structures nor in soluble RrgB produced in Escherichia coli or in Streptococcus pneumoniae is the D1 bond present. Experiments performed in live bacteria confirmed that the intermolecular bond linking the RrgB subunits takes place between the IPQTG motif of one RrgB subunit and the Lys183 pilin motif residue of an adjacent RrgB subunit. In addition, we present data indicating that the D1 isopeptide bond is involved in RrgB stabilization. In conclusion, the crystal RrgB fibre is a compelling model for deciphering the molecular details required to generate the pneumococcal pilus.


  • Organizational Affiliation

    CEA, Institut de Biologie Structurale Jean-Pierre Ebel, F-38027 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL WALL SURFACE ANCHOR FAMILY PROTEIN
A, B, C
605Streptococcus pneumoniae TIGR4Mutation(s): 0 
UniProt
Find proteins for A0A0H2UNM7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UNM7 
Go to UniProtKB:  A0A0H2UNM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UNM7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.192 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.619α = 90
b = 74.619β = 90
c = 340.527γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Other
  • Version 1.2: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description